My thoughts on having a SLF Sidewinder are that it cannot be hyperspace capable, although it could be capable of using supercruise. If you can swap out components in the Sidewinder, you should not be able to rebuild it in the fighter bay (similar to an SRV), as this would lead to a nigh unending onslaught of sidewinders with railguns. You should not be able to engineer the modules on the Sidewinder.
I think the best option here would be to allow players to buy a Sidewinder and kit it out, but make the players go back to a station to rebuy the sidewinder if it gets destroyed. For escort and utility duties, I think that the Sidewinders should be able to supercruise, but will need to dock with the mothership to go to a new system and that the mothership must drop from supercruise in the next system to redeploy the Sidewinders.
Putting a Sidewinder in the SLF bay should be a trade-off. Yes, it has the potential to be more capable in combat than a regular SLF, and infinitely more useful outside of combat, but if it gets destroyed you can't just rebuild it and launch another one, and the rebuy on it wouldn't be cheap compared to regular SLFs. Also, engineering the Sidewinder would allow players mitigate most of its weaknesses, and reduce the choice to "You Must Use A Sidewinder", and would completely break the game balance.
TL;DR: I think this is a good idea, but the Sidewinder cannot be hyperspace capable, cannot be rebuilt in the SLF bay, should be more expensive than regular SLFs, and must have some outfitting limitations.