I think Welling is the best choice available. When I think of who else is out there, I can't think of anyone who really fits the Superman role. As far as his voice goes, I wouldn't worry about it. I've seen interviews with Welling where his voice is much better. He purposely raises the pitch in Smallville to sound younger.
I agree that having the same guy playing Superman in two unconnected projects is a little weird, but it won't be a problem for most people. Smallville isn't very popular anyway. As far as the Superman movie goes, they need to pretend that Smallville doesn't even exist. If they have to many ties to the tv show, then audiences will get the impression that Superman 5 was just a bloated tv movie. That perception would kill Superman's potential to be a Spiderman like blockbuster.