Surely the best way to prevent pilots boarding capships is to only unlock fighters when in your own hangar, not in an enemy's. Only transports should be able to board enemy ships, and there should be no cappable flags on enemy ships (unless the objective is to assault a single command ship). So you have to defend your transport to sustain an attack.

If a guy boards it frustrates the pilots. If they don't want their capship damaged/destroyed, they'll have to land and fight on foot 'till the threat is gone. Or, the boarder's friendly bomber pilots who would get TKs for destroying the capship. You lose motivation to destroy a capship if there might be friendlies inside and that turns space maps into stupid boring infantry fights inside small corridors with constant lag due to moving capships.

EDIT: What gun is being held in that beautiful picture of that wonderful contraption you call "FS lollipop?"

This doesn't mean the TK risk doesn't exist. There's always gonna be an idiot that sits in the enemy capship too long.
Boarding is something that doesn't need to exist. It lags, it's frustrating and it pisses pilots off.
You also said that the capship fighting should be left to the capship's crew: Now I ask you: What the heck are you thinking? The capships crews usually get knifed while sitting at the turrets and then they're lost, they'll get spawnraped and the ship will have taken loads of damage through internal destruction. The pilots are still forced to take action. Boarding alarm? Hmm... No. That wouldn't help much. They'll still get overwhelmed by the sudden strike of an enemy inside and again, the ship's just lost to some people who can't fly and therefore need to piss everyone off.

Boarding is a bad idea, face it, and if you want inside capship fights, hope that there will be a inside a capship map. There are infantry only maps, so why do all space maps need infantry fighting? The only boarding that's good and not annoying is something like my map suggestion I posted.