I went through all of this myself last year when i decided to get a joystick.
Years ago when i first played Freespace i did it using only the keyboard and i remember being good enough at it. But after so many years, wanting to get back to Freespace, i found the keyboard very awkward. I could have given it a bit more time to get back into shape but the keyboard i have now has a different arrangement and lots more buttons on it and i don't like it. So i found Thrustmaster's "T.Flight Hotas X" in Argos(Ireland) for 36 euro and i went for it as that was about all i could spend on a stick at the time. It has a big throttle stick as well(removable) and 12 mapping buttons (+4 with the hat-left, right, up, down). It's a lot of fun to play with it but, yes, there is a big BUT....i bumped into accuracy problems. Self centering spring makes it very hard to move the crosshair with surgical precision, which so many times costed me bonus objectives in Freespace

I tried and took it off, following QuantumDelta's suggestion and while it makes it a lot better, it has a big drawback - i end up with a loose stick that's constantly leaning forward, causing my ship to pitch endlessly, making straight flying practically impossible.
So i put the spring back in, i adjusted the resistance to minimum, deadzone form the game menu to min and sensitivity to max and just tried to get used to it. I just finished playing Freespace2 minutes ago and having played Fs1, Silent Threat, Silent Threat Reborn(amazing!!!) and Fs2 on both easy and medium i still grab the mouse sometimes if i need surgical precision targeting.

Overall though it is a lot of fun playing with a joystick and if i had spent a considerable amount of money on my joystick i would have not accepted that lack of precision, but for 36 euro i can live with it. I know it's never gonna be as exact as the keyboard which you still need anyway for comm and other stuff like energy management, etc...
I hope you enjoy your new stick and let us know how you get on with it after you find your ideal mapping setup and get used to it.