First I thought about that two-window-solution as well. Hell, make the windows smaller or whatever - it's just for a couple of decades. Another possibility would have been to cut a new window once or twice a year and close it again. Ok, that would make a Specter each time, but since angels can obviously deal with them (they protect Mary in Cittagazze and Xaphania also allows will to cut that practicing window for her saying she would take care of the Specter), they could take turns or whatever neutralising a few dozen Specters more. There were still scores of them around anyway. After all Lyra and Will had done for them...
But the only truly romantic solution, of course, would have been to stay together in the Mulefa world for the few years they would have and not allow anything to part them again. At least I could satisfy my girlfriend with that one.

