For protection, is a special window needed in front of my FLIR camera that won't interfere with the thermal imaging?

Yes, germanium is a recommended window material for long wavelength infrared (LWIR) cameras such as Tau2, Quark2, Boson, Lepton. Germanium has very good transmission, but is relatively expensive.

FLIR sells an accessory option for its PathFindIR II product, a Replaceable Window Kit, that contains a germanium window 33mm in diameter (~1.3") and is 4mm thick. The Kit part number is 421-0055-00, and is priced at $300. 

Anti-reflection (AR) coated silicon is another option. AR-coated silicon is less transmissive, but less expensive.