I think you're looking at this from entirely the wrong angle. The Foundry needs to be MORE integrated with STO, not less.
We need things like direct access to foundry missions from the holodecks at Starfleet Academy. Or something like when you fly by a planet a little prompt comes up where you can access any mission that begins there. Or allowing us to create social maps, ship interiors and fleet starbases.
However, it's obvious to me that STO Foundry is no longer a high priority for Cryptic. It may get better after Neverwinter comes out, but for now expect requests and ideas to be ignored.
It's just in surgery atm. How well the patient recovers remains to be seen.
Hard to believe after three weeks, several big "maintenance" patches, the addition of Star Fleet Academy, and the patch to keep you on the grounds of SFA. All this stuff and the only word on Foundry is a message saying the foundry has been taken down "temporarily" with a link to click for more info that dead-ends at the STO homepage. If I were a betting man, I'd bet tomorrows patch doesn't fix Foundry either.
I know you don't believe this, but I'm hopeful for an eventual return of the foundry. But I also fear that fixing it might become a New Years resolution.
I'm assuming that alot of the work has been getting either the changes the foundry people made out of the code for now, or bringing the game side in line to use the already established code. Then of course is the chore of recovering the backups and redeploying, testing, etc. Its been a pain in the (redacted) but it is what it is. If anything its a learning experience I hope QA take to heart for future releases/branch merges.