You also assassinate an elder in Act 3.
The GTVA assasinated an Elder in a mission of peace with the GTA's own allies, using terrorists to cover up their tracks.
The UEF shot down a fleeing traitor.
Strap GEF's to flying bombs in the first mission, and in some cases, kill them.
Those pilots were known terrorists, part of a cell that's responsible for many innocent death'. Do you really think the general public will care much about them?
If you want something to put blame on the Fedayeen, better call them out for shooting down the UEF figher patrol that came to investigate the attack on the Vasudan convoy.
The Arethusa was destroyed under flag of truce.
As Suongadon already said, this was an accident. One that could have been avoided if the Deimos hadn't started jamming communications.
If you blew up the GEF habitat, that would have been a war crime, though considering we are talking about Kostadin cell here, it's still a far-shot from the bombing of Luna.
In short, yes the UEF and the Fedayeen in particular have done some very questionable things, but the GTVA is in no position to complain, seeing as how they did the same or even worse things themselfs.