He really should have surrendered. The only downside then is that the GTVA gets the Repulse, but considering it's probably low on resources/supplies anyway, it might not have been that beneficial to them.
Heck, considering BETAC probably has a lot of rules about the situation, 10000 officers and crew might be a rather hefty burden on the GTVA.
There's also no guarantee, if Koth were to surrender, that the entirety of his crew would have surrendered quite as willingly, and loyalists among the crew might try to sabotage key components of the ship to keep it from being useful to the GTVA.