Just because they have a huge sphere of influence doesn't mean they are very powerful. The Thalan love to build Embassies in the vanilla game, because they are easy to gain access to, and the Thalan don't have anything else to build early on. Take a look at how many planets the Thalan have, and how well developed they are. That should tell you, if the Thalan really are as powerful as you think, or if they are just a paper tiger.
As for their waships intruding your space, that is the case with all races. There is nothing you can do about it, except for declaring war and wiping them from the face of the galaxy.