Scoot, I hesitate to say good luck for the game in October... due to my wife being Cypriot I have to support Cyprus mate... It sounds like you've had some dodgy advice from your travel agent as I've driven the route from Nicosia to Limassol about 4 times in one day, it really doesn't take that long - 1 hour tops.
As for flights, you're better off trying one of the charter airlines flying out of Manchester. I personally always fly either with Helios or Cyprus Airways so I'm not too clued up on charters - I'd imagine people like Monarch, Air 2000 and Brittannia fly to Cyprus at that time of year. Another alternative is to book a cheap package holiday somewhere, if you're not massively fussy about staying in basic accommodation you should be able to find some reasonable deals. I'd also follow the advice given by others, stay at the coast, as there's not a great deal in Nicosia for casual tourists.
I'd agree with some others who have said that it is likely the game will be played as GSP just south of Nicosia. You can see it off the motorway as you drive towards the city so you wouldn't even have to brave the interesting driving of the city itself. I've been to a few Cyprus league matches at the stadium (being an Omonia supporter... well done Anorthosis ) and it's a good stadium. I'm not sure how the Cypriot supporters behave towards foreign teams but I'm sure it would be a less hostile audience than in domestic matches!
I'm sure you'll have an awesome time (and don't beat Cyprus too heavily)