I decided to replace the lock mechanism, got the bits off ebay, £15ish for the latch, £30ish for the barrel and cable section. The new latch works perfectly with just a screwdriver to turn it, the old one still doesn't. By taking out 3 pins from the old key barrel I was able to transfer this to the new setup without having to rebuild a key barrel! All fitted in no time at all and working perfectly.
I've beaten up the cable connector quite a bit and it's survived so I think it's pretty sturdy, though I seem to remember reading that they upgraded this component so older ones might still be vulnerable. I think the best thing to do is just maintain the latch mechanism. I thought about putting in a cable to the drivers seat, or something similar, but it just means anyone can open your bonnet. Likewise if you just leave the whole mechanism off and just use a large screw driver to turn the latch. I think you're just left with maintaining it, at least you know its a potential issue, and unless you've got skinny girl arms like me you're going to struggle to remove the latch from the inside, and I used a crowbar to finish it off.
No easy answers I'm afraid. My focus is a climbing surfing wagon, when it finally quits on me i'll scrap it, you probably treat yours a lot better!