You could add some cover in the middle of the cp. This cover can act as a wall to prevent a direct sightline. Any direct sightline from the spawns is a bad thing. Even when during a test it doesnt go wrong eventualy it will when other players play it. Its fully depending on the sniper behaviour.considering the concerns you've raised now and previously about this area, it adds weight to suggestions made by some others and have decided to go ahead and remove the windows entirely, roots and all, and i think it is the right choice. unfortunately, doing so creates a direct line-of-sight between red and blu spawn doors which is something i will have to address at some point.
I however still think that your glass idea wasnt bad at all and i rather dont see you remove it at first unless you already tested the change i did. If people still think they can walk through just add some props near that window that indicate its a wall. For example some wooden boardings on the lower part of the glass, or some fence. Still, i think glass does enough.