For SAP R/3 systems (or what you call ECC), your best bet would be executing remote function calls (i.e. RFC).
Normally these would be supported by open source interfaces for at least the more recent versions (e.g. 4.6 or above).
However, they are fairly scarce and I know only of one such implementation in R - this is the RSAP. You'd also need to download NW RFC SDK, and there may be further requirements based on your OS (e.g. what Visual C++ you'd need for Windows, etc.).
There's also a slightly more widely recognised equivalent in Python, the PyRFC.
On the other hand, you may try Robotic Process Automation (RPA) to interact with GUI in an automated way. One of the options is UiPath but there are others. This way you could configure the automation of table extraction - at the same time you can also call R scripts directly from the RPA.
Overall - to be honest - the solution with extracting tables into a separate database does seem to be the best alternative (compared to what I've described above).
Note: The above presumes that - for any reason, usually security - you cannot access the database underlying ECC directly through ODBC calls - otherwise the instructions for connecting and calling SQL from R are the same as for HANA or similar.