Vfr400/tbird wrote: But I'm worried the new battery might end up deformed as well, what causes this to happen is it normal if a battery is fully flat then recharged quickly ie a 2 hour ride at about 5-7000 rpm?

A battery shouldn't be allowed to run itself flat: lead-acid batteries aren't designed to supply high current for any length of time.
What they DO do, is provide a large amount of current to start the bike (known as cold cranking amps) for a short amount of time (ie. turning over the bike for about a minute), and then they are slowly re-charged from the current produced from your alternator when the engine is running.