I have seen this handled in a couple of ways. Option #1 is what I would recommend if possible.

1. Can you use REST API to return a list of the sys_id for the records you are trying to query for and then iterate through using gs.get to only get those records and make whatever updates are needed on the record?

2. Can you store your glideQuery results as sys_id in a JS associative array? I have seen these used mainly in conjunction with transform jobs but could see it being useful in other places as well.

-JB