This has already been repeated here...
First of all, Javi Martinez pushed back as CB is already a mistake, 2nd of all, there are many options better than Thiago in the case Javi plays CB, which is improbable unless Pep is crazy when the current defense is good enough.
More to the point, if a system involving Javi at CB is adopted, (which is not at all unrealistic, we can argue about its merits some other time) it's quite likely that Thiago will get a lot of minutes and may become a part of Pep's 'ideal XI' . They have a stacked squad and I'm sure anyone could come up with plenty of good looking lineups that don't involve Thiago, but that fact hardly shows that he is now doomed to warm the bench.
If Javi stays in midfield though, it'll be with Schweinsteiger and Thiago finds himself competing with Kroos/Muller/Gotze for two spots, and that's assuming Ribery + Robben is still a permanent fixture, which I don't think is a certainty.
Basically ou have to assume Javi won't play CB, Ribery and Robben will both start all the time, and Gustavo/Kroos/Muller/Gotze are all certain to be higher in the pecking order than Thiago in order to conclude that he's definitely going to be starved for minutes.