Spurs will certainly be without Kyle Walker on Thursday. Pochettino said that he is out indefinitely, but he is the only confirmed absence. Danny Rose is also battling a small injury and may miss the match,
Capoue has been tremendous for Spurs this weekend and was at his best in Tottenham's 1-1 draw with Arsenal on Saturday. He has locked down the midfield and, despite some pretty strong competition, is the unquestioned first choice central midfielder. He has been that good.
The good news is that Capoue seemed unlikely to play on Thursday anyway. Pochettino has been rotating the squad for the Europa League and Benjamin Stambouli and Nabil Bentaleb were good bets to start against Besiktas regardless of Capoue's health. Even if Capoue cannot play, there is no major harm done.
The way Pochettino talked about Capoue's status seemed to indicate that there was no concern it would be a serious or long-term injury. So long as that is the case, missing one Europa League match is fine. Tottenham can breathe easy.