Take burst weapons (Plasma Accelerators, Frag cannons, etc.) and quickly burst him then fly out of his line of fire while you reload or just spin in circles, believe me, gimballed MCs HATE that!
The problem with frags is that they do less to almost no damage at long range.
The problem with PAs is that they are easy to dodge at long range.
Oh well, can we get seeker version for the PAs, please?
There's no counter. With proper throttle control and FA-off an FDL can keep range and face-tank any ship. Then it's just down to DPS/HP
Short story: I agree with Alexander.
Long story:
It is about 2 months I have switched to full time PvP and, taking into account the amount of commanders (all sizes, all ranks) I have beaten, iI believe I'm good

I use an armored shieldless FAS with triple frag canons and a single large beam. Deadly but...I need to fight at close range for max efficiency. It has some drawbacks but boost+ram and frags at point blank do a ton of damage, allowing to take down commanders pretty quickly (AKA: before they high-wake or combat-log).
Fast reversing ships with strong shield keeping 4 pips to SYS is my nemesis...not that I feel threatened by them since they don't deal much damage if you don't face them + go into a straight line, and I can get away anytime, but I haven't found any proper method to beat them.
Yesterday I faced a very skilled FdL reversing commander and I lost 2 fights to the death (actually 3, but something really weird happened during the fight). Like people mentioned, boosting like crazy toward him while zigzagging / using vertical+lateral thrusters works to dodge fire and get closer, but these damn FdLs reverse pretty fast making it pretty inefficient. And remember, I am shieldless which means I can keep 4 pips to ENG and 2 to WEP...players with a shield would not be able to keep 4 pips to SYS and enough pips to ENG/WEP to boost and fire efficiently... The fights lasted pretty long and I still managed to deplete all his SCBs but by that time I had only 10% hull left.
Of course, after a so long fight once the SCBs are depleted and shield is down, a fast FdL would high-wake...so I guess the best method when I face this will be to simply not fight if I see after a minute that it is not going anywhere
So...Did you use Chaff?
Tried silent running?
If all he used was multis and gimballed at least that could have screwed up his aim and he would have to go manual aiming while FA-Off.
I use both Silent Running + heat sinks, and chaff.
Keep in mind that as soon as you open fire in SR, your opponent can use gimballs (though the firing cone is reduced) and see the reticule for fixed weapons (that FdL commander taught me that). So if you use it offensively like me, you must not fire until you get close enough (which is hard to achieve if he reverses at high speed), and disable SR. Chaff becomes then handy.