No, thread stacks do not use memory in the buffer pool, they use the non-buffer memory.
CLR disabled does not mean no CLR. The system assemblies can still be used. There's a lot of other things that use the non-buffer memory as well.
Gail Shaw
Microsoft Certified Master: SQL Server, MVP, M.Sc (Comp Sci)
SQL In The Wild: Discussions on DB performance with occasional diversions into recoverability