You can do prone holds etc - but the exercises your doing on the reformer should be fine. Have you had a recent Wikipedia reference-linkMRI - is it still prolapsed or is it reducing?

Post meniscal arthroscopy you should be moving pretty quickly. Generally returning to sport within 5 weeks. and starting running etc by 2-3 weeks.

If you can use a spin bike without leaning forward then thats ok - but how about a cross trainer? it'll allow you to maintain your lumbar neutral much easier. And definately get into the pool. Thats brilliant exercise.

Good Luck