Well,
1) The ship wouldn't be exactly free. It'll still take a month or two to repair all the damage. If it's an alien ship, then it'll take even longer because scientists and technicians would have to study and possibly reverse engineer several of the controls. Hell, they'll need to study the alien language first as well.
2) I'm pretty sure every ship, or at least every destroyer are stationed with their own marines for such scenarios. Just look at the menu screen, you can see armed marines guarding doors.
Unless you have specialized tools, it won't be an easy task.