I’m not going to discuss whether it’s politically correct; because I don’t know; but why? Regardless of the facts on paper, I think we all know why..
Government took him into custody at great risk of international influence and potential blow to the vote base in the General Elections due in April. It has already provoke questioning from world powers and some significant protests from the masses; in contrast, knowing Sri Lankans - and the international community, had they done this in another couple of years, the effects would have been almost negligible. So why now? Why risk all this?
Fonseka was threatening to go to international courts with cases against Sri Lankan army (i.e Gotabaya Rajapaksha and the Army Generals who were not in his side at the elections?) on human rights violations. He had already made serious allegations and brought too much attention and unease to the government. The opposition leaders and the LTTE sympathizers had already been doing that, but that wasn’t received as seriously as Fonseka’s allegations by the world powers.
There’s nothing pretty about any war. And the war against terrorism in Sri Lanka probably had its ugly turns here and there which Fonseka knows, and the government knows too. So the government didn’t probably want Fonseka to keep talking, however untamed his speeches are, he still has some credibility as the ex-army chief. Especially, since he was seeking asylum in countries like Australia, where he would have the opportunity to rehabilitate himself to be more politically attractive the government must have thought that the damage he could cause while being out is much greater than what it would be if they arrest him.
Secondly, if he is to be brought in-front of the law, the government probably has much more control over the military law than the civil. And in order to charge him under military acts, it had to be done within 6 months of his retirement.
I think the charges that the government has against Fonseka are serious enough if they prove them; I don’t know whether he really did them, but the idea of overthrowing the government probably went through his mind while he was in uniform - but again, you can’t charge him for having the motive alone...
All that said; I think trying to compare Karuna and Fonseka is immature and lame. Wars are won because of tactical decisions than moral decisions. Karuna was (and still is) irreplaceable for his political as well as military value. Fonseka as the army commander, always was replaceable.