I never reference a form control in a saved query unless it's absolutely necessary, for the very reason you've encountered -- it makes the queries less widely usable by virtue of the outside dependency on the form being open.
Access provides multiple ways of applying criteria to recordsets at runtime, so there's almost never any need to hardwire a dependency on a form control.
That said, if you can connect to your database with DDE, it should be able to do the job. DDE used to be the default for Word merge from Access databases (to my eternal annoyance). It launches a new instance of Access (which means that if you have user-level security in place, it will sit and wait with a username/password prompt and never open your database), and then communicates with it via old-style DDE commands. In your case, it ought to work if you open the needed forms in your database's startup utilities. However, if they need to have data filled out by the user at runtime, then that won't work, either.
The ultimate solution is to decouple your saved queries from the forms, or to use the raw SQL string within Excel to retrieve the data (absent the form reference).