jonny,
I think you may need professional tax advice - there may well be a way to efficiently transfer the value of your pension fund to Ireland. If you are coming to Ireland as part of a relocation package, maybe your company could pay for the tax advice.
I would be surprised if the Revenue only taxed you on the gain since you were resident in Ireland - what you are talking about is Capital Gain tax and this is calculated based on the selling price minus the purchase price - I don't think it matters where you were domiciled when you "bought" - however, I am far from an expert on this matter and there's a good chance I am completely wrong!
Alternatively, would it be possible to leave the pension offshore and recieve the benefits on retirement?
I think a lot will depend on the offshore location ie the laws are different on Guernsey than on the Caymans
BTW - €50k+ pension fund after three years ? - Nice Job! - given the salary level that would be needed to fund that level of pension over three years you should definitely be getting professional advice (IMHO)