The "fanbase" argument is another false argument. WB is about making money, not appeasing a bunch of whiny fanboys. "Splitting the fanbase" is not on their list of priorities, trust me.
The bottom line is Smallville makes money relative to its cost. Superman Returns didn't.
Now, I'm not saying WB will cast Welling in a reboot (I get the feeling any rebooted movie will be from scratch), but I am saying that his involvement in Smallville (or his reputation with certain fans) isn't going to mount to a hill of beans in the grand scheme of things.
In fact, I'd think that his Smallville connection should, in a just world, actually help his chances for a Superman movie.
The bean counters aren't stupid. They know creating a movie with the budget of Superman is going to be astronomical. Singer proved an already astronomical budget can grow ad infinitum in the wrong hands. They also know what their television division is doing on a weekly basis up in Canada on a slashed production budget. Which one gives them more bang for their buck?
In our economy, which do you think is the smarter choice?
--Hire a complete unknown as Superman, pair him with a big name director and screenwriter who has a vision for the franchise, pull in the top FX houses and a budget of more than $300 million.
--Hire a known quantity with a background with the character, port over the television crew and producers, maybe tag an acclaimed comic scribe (like Geoff Johns?) and give 'em a budget of $150-$175 million.
The first option is the classic high risk-high reward. If it's a smash, then great! But, you're going to have to make an awful lot of money to get any of it back (which was SR's problem).
The second option is the safer route. Even if it isn't a gigantic hit and only barely makes $200M (again, like SR), it'll still make a significant amount of money, relative to its cost. But, because the producers and financiers don't come out of it in the red, you're able to build on the success a la Batman Begins begetting The Dark Knight.
Who knows where WB's mind is now? There's going to be a lot of infighting between divisions, but I don't think anyone in charge really gives a rat's ass about certain factions of fanboys and girls.