3. These factors increase farmer suicide
That may be some truth to that; but it's not entirely fair to blame it on "GMO" crops, because:
- The evidence is that Bt cotton generally (i.e. on average) performs better than non-Bt cotton
- When and where Bt cotton crops failed, that was not the fault of the Bt trait (it was more caused by inexperience with using it, per this answer)
- Statistics don't show a strong correlation between suicides and the Bt cotton: as follows.
The article referenced in the OP says,
The region in India with the highest level of farmers suicides is the
Vidharbha region in Maharashtra -- 4000 suicides per year, 10 per day.
This is also the region with the highest acreage of Monsanto's GMO Bt
cotton. Monsanto's GM seeds create a suicide economy by transforming
seed from a renewable resource to a non-renewable input which must be
bought every year at high prices.
The Bt Cotton and Farmer Suicides in India article (the same as already referenced in other answers) says, about the Maharashtra state,

For Maharashtra, the combination of suicide and adoption rates leads
to similar conclusions (Figure 12). Maharashtra tends to be a good
proxy for what happens at the aggregate national level, notably
because of its important cotton sector. Figure 12 clearly shows that
the growth in farm suicides in this state started much before Bt
cotton and actually slowed down in the years after the introduction of
Bt cotton. Even the relative peaks in suicides observed in 2004 and
then in 2006 lie under the projected trend line from 1997–2002.
Overall, at this level of analysis, all other things being equal, it
is clear that the overall adoption of this technology was not a
driver of suicide growth; in fact it may even have helped slow the
process.
The data shows that suicides have been increasing, and continued to increase (slightly) after the introduction of Bt cotton; but, that the rate of increase has slowed.
Vandana Shiva, who is the author of the article cited in the OP, ends the article with a recommendation:
The suicide economy is not an inevitability. Navdanya has started a
Seeds of Hope campaign to stop farmers suicides. The transition from
seeds of suicide to seeds of hope includes :
· a shift from GMO and non renewable seeds to organic, open pollinated
seed varieties which farmers can save and share.
· a shift from chemical farming to organic farming.
· a shift from unfair trade based on false prices to fair trade based
on real and just prices.
The farmers who have made this shift are earning 10 times more than
the farmers growing Monsanto's Bt-cotton.
In Navdanya : An Overview it says,
Navdanya has trained about 500,000 farmers, conserved 3,000 varieties
of rice.
Navdanya's seed bank in the farm at Dehradun preserves 500 land races
of paddy, 150 land races of wheat, 11 land races of barley, 5
varieties of barnyard millet, 10 varieties of oats, 6 varieties of
finger millet, 3 varieties of foxtail millet and 7 varieties of
mustard.
Biodiversity Conservation
Till date Navdanya's conservation farm has protected 12 genera of
cereals and millets, 16 genera of legumes and plants, 50 genera of
vegetables, 7 genera of oil yielding plants, 13 genera of spices and
condiments, 20 genera of aromatic plants, 54 genera of fruit and
flower yielding plants and 250 genera of ornamental, timber and
medicinal plants.
And on its home page it says,
Navdanya has helped set up 111 community seed banks across the
country, trained over 5,00,000 farmers in seed sovereignty, food
sovereignty and sustainable agriculture over the past two decades, and
helped setup the largest direct marketing, fair trade organic network
in the country.
So, apparently Navdanya advocates that farmers should grow various foods. If "they should grow food instead of Bt cotton" is true, the main point would be that it should be instead of cotton not instead of GMO.
I understand there are arguments for food sovereignty and fair trade, perhaps even for organic agriculture.
However, her writing a polemic against (specifically) GMO instead of against (more broadly):
- Monocultures
- Practices which require (borrowed) money or large capital investments (e.g. for irrigation) as their input
- Crops which have variable/risky rates of return (e.g. water-dependent cotton in areas which rely on rain instead of having artificial irrigation)
... may be doing her argument a disservice: because, the mere fact that it's GMO doesn't seem to be the villain in this story. For example the question posed in the OP, and Sancho's answer to it, fixate on the question of "GMO crops". But the article is actually talking about a different time-line, for example:
200,000 farmers have ended their lives since 1997.
In 1998, the World Bank's structural adjustment policies forced India to open up its seed sector to global corporations like Cargill,
Monsanto and Syngenta.
1593 farmers committed suicide in Chattisgarh in 2007. Before 2000 no farmers suicides are reported in the state.
Bt cotton wasn't started to be introduced until 2002.
Some of what she said is supported by the article, for example my highlights in the following fragment:
Monocultures and uniformity increase the risk of crop failure, as
diverse seeds adapted to diverse to eco-systems are replaced by the
rushed introduction of uniform and often untested seeds into the
market. When Monsanto first introduced Bt Cotton in 2002, the farmers
lost 1 billion rupees due to crop failure.
However, those are temporary problems. At best, the truth of what she's saying against GMO in general (i.e., not temporary problems) may lie in some of her other allegations (which I haven't disproven): for example that GMO cotton can only be grown as a monoculture and precludes diversity -- not simply "diversity of cotton varieties" (there are many varieties of cotton with the Bt trait), but "diversity of crops" including non-cotton food-stuffs.
The cited claim, though, may be true:
High costs and unreliable output make for a debt trap, and a suicide economy.
Although Bt cotton improves the average profit of cotton farming, it may not be suitable for farmers who must borrow money to afford it, and who can't afford/survive occasional years of losses.
Some of her other allegations may also be true: for example, complaining about cotton subsidies in the USA ... but again, that's not specifically to do with GMO.