You might get a break with the verbiage used in writing up the regulations.
For example, see if you can have them say the trail is closed from dawn to dusk to "recreational use". Be sure that they speel out that commuting is not recreational.
They get their enforceable code and you get to use the trail. If the local governements have any "most liveable city" or "clean air" initiatives, going on, you might find some backup from the folks in charge of those, as a rail to trail project is a pretty cheap way to make some headway on either of those.

Good luck, I hope you get your way. I'd love to see some tracks here converted for bikeage.