I changed the drivers side engine mount, but as i was doing up the bolt, I threaded it.

Would it be a matter of just re-threading the hole?

How safe would it be to drive with just the two nuts?

See picture. (the bolt in the middle)

http://imageshack.com/a/img742/7426/vzQwqq.jpg

That centre bolt is a real problem waiting to catch you out. I did the cam belt on my TJ, bolt came out with alloy all over the threads. I just forced it back in. When I did the cam belt on my TL, the same - this time, I had the hole helicoiled. I guess you could just run a tap down the thread, clean the alloy off the steel bolt, and bolt it all up. I don't know why this hasn't come up more often on this forum, to be honest.
As for just leaving the bolt out - someone else will have to comment on the safety aspect of doing that.

I have run a car with 3 of the 4 studs, but there is a huge amount more load in this situation. Might get the shop to do this one as I don't want to ruin the block.

Is ok short term. See many like this,

Hehcoil Is your best bet. 12 × 1.25 from memory

Always use anti seize on these bolts.

The previous owner of my car or their mechanic threaded the same hole, I just put a new motor in :p

But I was thinking about a helicoil too.

Haha I was thinking oh great I've ruined the block, time for a 75