We just did this...
We had the double pain glass windows - worst of all...
Best way... put a stone bit on a dremel and grind a slot in the inner glass big enough to put a blade screwdriver in. It'll take a while and the glass will get hot. Be ready for it to shatter. DO NOT TOUCH the outer window. Tape across the window with some packing or masking tape - several times.
Now, make sure you've got appropriate protection, put that screw driver in and break the glass. Pick all of the glass out (wear appropriate gloves) and pull the sealant out between the two panes - all of the way around. This was the hard part.
Clean the window nice and pretty, clean the seal and anything else you can while you're there.
We took some backer rod (very firm foam rod - 1/2" in diameter) and wrap with with an appropriate outdoor fabric - we used AllSport 4-Way Stretch Premium Marine Vinyl (I forgot where I got this hint). My wife glued the fabric around the rod, then we pressed it in with the seam hidden in the slot. It put fair pressure on the window holding it out. I will put a coat of sealant on the outer window seals soon.
Be forewarned, I broke an outer window before I did the dremel trick. In fact, I had the inner window out and was happy when it was done and looking nice. Next morning my wife tells me the out window shattered - I must have tapped it with the center punch.
We replaced that with lexan. Hopefully it holds up.