Not sure what your issue is. Most people are terrible at maintaining their deps. Suffice to say, have you tried switching to ngx-md which is the advice given on the deprecated angular2-markdown npm page - https://www.npmjs.com/package/angular2-markdown
I had a similar problem when upgrading to ng6 with a diff package. I aborted the ng6 upgrade. Switched to the new package. Then did the ng6 upgrade and it worked. Not sure the best approach for you but when you do the ng6 upgrade there is a lot of moving parts so best to reduce the amount of changes being made by doing as little at a time as possible and then testing it and saving to git before moving to the next part.
Also, I hope you did the ng6 upgrade using ng update as described on the ng6 page here - https://blog.angular.io/version-6-of-angular-now-available-cc56b0efa7a4
PS You don't mention an ng6 upgrade but the rxJS 6 upgrade comes for free with the ng6 upgrade hence the assumption sorry if it is wrong
PPS Are you using rxjs-compat which will allow you to upgrade to rxJS 6 whilst still allowing some parts of your code to use the old approach thus preventing breakages. Again this comes for free when you do the ng6 update - the link above talks about rxjs-compat BTW