If we stay with the standard FS way of doing these things, meaning that Fighters won't be able to destroy a capship, only specific subsystems, it's going to work allright, I believe.
As for the Rebels capturing Ships, for obvious reasons (personnel and maintenance, for example) they don't have that many Capships. The few they do have are either purpose built (like the MC-80), were captured in combat or defected outright. As for capturing, I think the biggest one they did catch was Lusankya (a SSD), but that was after the Battle of Endor. Before that, the Rebellion couldn't afford the big capships the Empire built (As one of the WEG sources put it, "A Star Destroyer is 800000 design mistakes waiting to be exploited"), and thus didn't even try to acquire them.