Invading other sovereign countries is frowned upon, by and large. I know the Geneva Convention as well as I know Cuban history, but I'm pretty sure it doesn't go down well.
I think the idea of sovereignty is flawed if it tells us we're supposed to let dictators like Castro stay in power. Why should we respect the sovereignty of a dictatorship when they have no legitimate reason to be there in the first place? If the US could get rid of all the dictators in the world I'd want us to do it tomorrow. Now for a lot practical reasons, invasions and embargoes are rarely the best way to go about this, we can't just go around invading every country we don't like. But the idea that it's illegal for us to help an opposition group overthrow a dictator I think has its priorities all wrong.

PS: The Geneva Convention has to do with treatment of civilians and POW's during wartime, it doesn't have anything to do with whether the war is justified in the first place.