If there's a team where Thiago has less chances to play than Barcelona, it's Bayern.
And I doubt Pep will just move Javi as CB unless Boateng starts fucking things up very badly.
Also, they can buy Inigo Martinez as CB since Badstubber is also injured ( till? ).
Thiago is far form Bayern's level, it would be a mistake if Pep forces him in a 11 with clearly more valuable players than him for now. At least in Barca he might've had some chances rising soon, in Bayern I don't see him in a good position for now. Maybe the will loan him to a mid table Bundesliga team by winter.
They can also try transferring Thiago Silva in 2014-15, so they can upgrade Dante and buy some more players form Borussia to kill everything in their way, plus Borussia has it's limits, may not be able to fulfill the desires of most players form there.
---------------------Neuer--------------------
--Lahm----Silva/Dante-------------Inigo/Holger-----Alaba---
-----------Gundogan/bastian-------Javi Martinez---------
--Robben/Blaszczykowski---------Muller/Gotze-------------Ribery/Reus----
--------------------Lewandowski/Mandzu-----------------
Where is Thiago here? At Bayern B? Maybe Borussia...a.k.a. Bayern B
.
10-0 on Allianz/6-0 on Camp Nou easy, vs Barca.