yeah it’s a tricky one – the old city is definitely worth a look, especially if you like crowds – but it’s not really compatible with ‘decent pubs for a couple of beers’. That’s a bit like asking for a decent pub near Buckingham Palace…
I haven’t been to Prague in a couple of years but if I wanted a chilled beer I would probably hop on the Underground to Jiriho z Podebrad and wander towards the TV tower (worth a look in itself) – lots of nice neighbourhood bars around there. Or the street called Ujezd, at the bottom of Petrin Hill (which is also well worth a wander up, use the funicular to get up, then walk down!).
Oh yes – if it’s hot then there are 100000 outdoor bars to enjoy. My pick is in the park called Letenske Sady, it overlooks the city (just on the north side of the river), very pleasant to look down onto the city with a beer of an evening 🙂