To prepare any spell, a wizard must have enough peace, quiet, and comfort to allow for proper concentration. The wizard's surroundings need not be luxurious, but they must be free from distractions. Exposure to inclement weather prevents the necessary concentration, as does any injury or failed saving throw the character might experience while studying. Wizards also must have access to their spellbooks to study from and sufficient light to read them. There is one major exception: a wizard can prepare a read magic spell even without a spellbook.
As you've tagged this rules-as-written, I'm going to skip all the side-stuff other answers discuss and get straight to the point: if the wizard fails a saving throw during his preparation, it is interrupted. While there's no guidance exactly for when a disease's daily saving throw should go off, most GMs choose to make that roll during the character's sleep - which does not interrupt rest, per the paragraph above the linked one, and so doesn't affect spell preparation - or they have it go off at the same time of day the first roll was made - which almost certainly is not during spell preparation, either.
A GM is technically within RAW to call for the save during the wizard's spell preparation, but is likely to be judged unnecessarily harsh or vindictive for doing so; and even if the wizard fails the save, nothing prevents the wizard from simply starting over. Unless there's a serious time pressure preventing the wizard from spending an hour and a half instead of an hour preparing spells, all you successfully did was manage to annoy a player.
Mouhgouda's suggestion of allowing a concentration check in the case of a failed save during spell prep is a good one, by the way. It's not strictly RAW, but it's an excellent and simple houserule.