Leedoak,
That's great. It's a funny one with the MLD because typically guys/gals can't do the PFA or CFT. However, once you've got it under control and know what you need to do to exercise you'll still be fine.
If the RCMO is onside that's great. When the medical reviews happen at Regiments the CO, OC's and doc will go through each case. The CO is the one who needs to be convinced and will take his lead from the inputs others give at the reviews. You are right to think that the Army wants deployable troops, but I'm 90% sure your pension will be safe.
It's a lot to take in at the start and I know career concerns can be a real worry (life changing obviously). I'd recommend looking at the MOD tri service documents (I can't remember their abbreviation!) which covers discharges etc, so you can see what may/ may not happen in the future, what boxes need to be ticked and how to play it so you've the best shot of staying.
I'll keep my fingers crossed for you and if I can help at all feel free to message me.