Coincidentally I was think about the opposite, going from manual to auto. Sure either way it would be a bit of a job but not impossible if you have all the bits and are reasonably handy with a set of spanners.
But in your case there are plenty of manual cars and it would make sense to hold out for a good 5 speed car. I my case not so easy as automatics are few and far between and I've never seen an auto GTI in the UK so a swap would be the way to go.