In Smith and Jones the Doctor said that if the Judoon found the hospital guilty of harbouring a fugitive, they would sentence them all to exacution. So, my question is, they found the fugitive, so why weren't they killed?

He said if they DIDN'T find the fugitive, they would all be killed. They did, so no sentencing!

Probably because there was no time. The plasmavore had already started up the MRI by that time, remember, and so sticking around to zap everybody would not only endanger the Judoon but would also be pointless, since the MRI was pretty much a death sentence anyway.

I think it's because when the Judoon found the "Fugative" he was already dead, and one of the "Humans" killed him, so that justified them not being executed. But that's just what I think, so it's probably wrong!

no the alien's in the hospital don't kill the people in the hospital live the doctor gave his life!!!! that is SO the doctor!!!!

For start he says "could", not "would".
Plus, why would they have found the hospital guilty?
Martha helped them find her the Plazmavore. She wouldn't help them if she wanted to hide it, so they had no reason to prosecute.

Because the Judoon had to evacuate and quick!!!

And i think because Martha showed them they didn't think that it was thier fault she was there?

they did find the fugitive and did not kill them. because they would have killed the source of information.