I don't think you can side with Bodhi if you take the thief stronghold assuming the EE hasn't changed things.
If you just mean going back after you've killed Bodhi and taking out Aran Linvail, then... well I don't quite remember. I think you would still have to deal with Arkanis Gath at that point, and it's possible Renal Bloodscalp would become hostile. Which wouldn't mean you lose the stronghold automatically, but if for some reason you fail to pay Joster you wouldn't be able to go to Renal to get reinstated.
I'm just totally going on (long unused) memory here though and I could be completely wrong.
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If you just mean going back after you've killed Bodhi and taking out Aran Linvail, then... well I don't quite remember. I think you would still have to deal with Arkanis Gath at that point, and it's possible Renal Bloodscalp would become hostile. Which wouldn't mean you lose the stronghold automatically, but if for some reason you fail to pay Joster you wouldn't be able to go to Renal to get reinstated.
I'm just totally going on (long unused) memory here though and I could be completely wrong.