The frequency does not have to be spot on but cannot vary that much, I suspect problems with similar pumps in the past were due to them being driven at 130% the speced frequency (67 Hz instead of 50).
Mostly likely the problem is driving an AC motor using a squarewave AC signal. AC motors require Sine wave AC to run properly. Other wise they over heat caused by core saturation, or they will blow your bridge Mosfet when the current demand soars due to core saturation. It should be powered using a sine wave. Since the current is very low, you might be able to drive using a BTL (Bridge tied load) circuit.
The original controller uses 4 N channel mosfets in a bridge formation. the circuit drives a reciprocal pump, presumably the original one uses a switched capacitor boost circuit to produce the drive for the N channel mosfets on the positive side.
The best option is to use a pair of half-bridge Mosfet drivers. Mosfet drivers will protect your MCU from voltage spikes that are generated by the motor. Ideally you connect the the MCU to the half-bridge drivers using a 10k resistors and a small TVS diodes to ground so that the MCU does get fried, in the event that the voltage spike exceeds the half-bridge drivers voltage rating. Most half-bridge drivers can operate up to 600V, (some up to 1200V), I have seen instances where a 36V H-Bridge driving an induction load exceeded 600V, blowing the half-bridge driver and taking out the controller when it fried.
well it's for a military thing and is already a replacement for another cockup we made in supplier choice, punch through must be non existent I'd say as they're talking potting this thing or at least putting it in a box (that does into another larger box) so the dissipation that punch through would cause is a bit no no
Wow! No EMP\EMF protection, no RAD protection, using commerical components! Hope this isn't for use in NATO!
Shoot-through can be avoided using half-bridge drivers that have shoot-through protection (ie will not permit the high-side and low-side from being turned on at the same time). That said its still possible to have a shoot through issue if you don't discharge the MOSFET gate fast enough. Its possible that you turn off one transistor and start turning on the other transistor before it full turns off. Dead-time is added to protect this from happening. Gate resistors should also have a parallel diode so that the MOSFET turns off faster than it turns on all four mosfets should have a 10K resistor connected between source and gate to prevent the MOSFET from automagicially turning on when you don't expect it. If the gate is not held low, a MOSFET will slowly turn itself on, usually with disappointing results!
it needs to be as small as possible so unless the driver chip can also generate 50Hz it's a nogo, I'm hoping to show him something (on a PCB) when he comes back from holiday so have to use what I have.
Your not going to be able to drive a MOSFET directly from an MCU, especially if its a 3.3V MCU. You might be able to get away with a logic level MOSFET, but they are more prone to failure, especially when switching inductance loads. Your much better off using a pair of H-bridge drivers. If size is a problem, there are drivers in DFN packaging. You can also use dual sided component boards to reduce PCB size. You can also use the smaller DirectFET packaging now available. If size is very restricted then you have to implement a PWM Sine wave logic drive to power the motor:

BTL requires a pair of inductors and caps, which take up lots of space. Plus Electrolytic caps aren't milspec unless you get an exemption.
Here is an half-bridge MOSFET driver in a LLP-8 (4 mm) package
http://cache.national.com/ds/LM/LM5109A.pdfand then if he insists in burying it in resin
Perhaps to hide the design, since its not milspec. FWIW: I would not touch this project. If its for the miltary and not Milspec and quoted as Milspec, you could end up doing some serious jailtime. If he gets in trouble, than passes the buck onto you blaming you for the poor design. I think this project is over your skillset in my opinion. Hope it works out though.