Tape off the glass with painters tape. Tape off the wall. Take out the sashes. Stain. You might want to use a fast drying water base stain. Put the sashes back in. Next day, remove them again, then put your finish coat on. Let it dry for a few hours. Replace the sashes. Remove all the tape. Take your time, be neat, wipe the stain with a rag for even coating. Should be fine.

Get another contractor, that one is an ass.

Also get another brand of stain, try either Minwax, or Benjamin Moore, Sherwin Williams anything but that crap Behr. i would suggest a true paint store as well because you may need to mix several stains to get the exact color you need.

also pine and fir will both take stain entirely different and look like completely different colors even using the exact same stain

I second that - don't use Behr. Every year I put Behr 10 year stain on my deck. lol!!

I suggested water base only because you don't have the strong odors.

Get your stain from a place that will custom mix it for you, and take both pine and fir pieces to them and have them play with it to get the colors the same. And remember, a little goes a long way - you probably won't need a gallon of it.