I think there's literally 0 chances of Boa being captured. The only reason for something like that would be to do a rescue arc and this ship sailed when Sabo escaped. Outside of that, it would be just a bleak ending for a ally of the crew. Specially because Coby is also some sort of Luffy' ally.
Add to the point is that this is a idea endorsed by Fujitora and nothing he does goes as planned. Boa is safe.
I do think Boa probably gets captured. But i'm 100% sure that coby ain't gonna be the one to defeat her.
The opposite will happen. He will either defeat her or oda will have them come to a tie with neither being able to take out the other. Reason being is so that we can also get her powers fleshed out. With this coby jumps up to vice admiral rank before the final war with Boa escaping to regroup and grow stronger to also participate in the final war. It would be a win win for both Boa and coby fans.

Or . ..

If not then he (coby) is going to be responsible for stalmating her (they both knock each other out) with the rest of the Marines present capturing her since she would be unable to fight. This puts a huge dynamic on both coby and luffys relationship.