I suppose it would depend on what grade of MCL sprain he had, and that you may be right if it were anything other than a grade 1, but it definitely doesn't sound too serious judging from the reports, especially if he took part in a limited practice on Wednesday--less than 48 hrs after the MNF game vs DET.
One would think that if it were that bad that he couldn't play on Sunday, he probably wouldn't have been a limited participant in practice on Wednesday, but I'm just speculating like you are. I would think that if it were an injury that could potentially hold him out of the game on Sunday, he'd probably not be practicing on any level, not only Wed, but also Thurs, and even Fri too. We've seen plenty of QBs miss practice for a couple/few days during the week, yet Flacco didn't. I suppose it's certainly worth keeping an eye on tomorrow.