Finding Repetetion rate of ns pulsed waveforms
problem statement: my sampling rate would be 2MSPS - to acquire a 100ns pulse i require that much


Nope. 100ns is 5 times as short as the interval between two sampling instances in your sampling device. If it does indeed measure the voltage accumulated over a capacitance, this might work – if that capacitance is as small as possible, which it often is, you might just miss pulses.

However, you're right, the signal you're interested in actually doesn't have a bandwidth of 10 MHz – the maximum frequency of interest is 50 kHz, so observing a system that indicates the presence of a pulse (not the pulse itself) with a 100 kS/s sampling rate should suffice. 

If you know you just got presence information (i.e "there was an impulse during the last sample time, or not"), an FFT is a bit over the top. Simply count the samples between an observation.

The hard part actually would be the electronics to your photo diode – 1ns impulses imply that your system needs to have a bandwidth of 1 GHz – so you'd be deep in the world of RF/microwave circuitry. What you'll probably end up doing is amplifying the current coming from your diode, with something avalanche-based, or a sensitive microwave transistor. Don't forget to lay out your board following the needs of a microwave signal! You can't afford spurious interference here.

You'd essentially amplify the energy of the pulse. The voltage over a simple RC lowpass fed with that energy with a 90% discharge time of let's say 1/(100 kHz) would serve as a feasible indicator of activity; observe that, if you want with 2MS/s, and you'd have captured a signal from which you can directly see the impulses.

Notice that photodiodes with a > 1GHz bandwidths will be noisy, so you'll probably have some false impulses. Here, your FFT approach might actually tell the periodicities from the white noise.