To re-cap the FAQ states:
Q: Does Warptime allow the psyker to pick and choose
which To Hit and To Wound dice he will re-roll? (p88)
A: No. He can decide after each To Hit or To Wound roll
but he must re-roll all dice or no dice
I'll be honest, I've never used it like this, nor have I seen it played like this, but the FAQ is pretty clear. All you're now mitigating against is a particularly bad set of rolls like 5 misses or similar. Given Warptime is reasonably pricey in points, IMO this is not worth it.
At a small tournament last month, I dropped Warptime in favour of Wind of Chaos which is more points than Warptime (30 points IIRC so 5 points more). I did find it useful in most games and I think it probably made it's points back in most cases.
Alternatives for a Nurgle Daemon Prince are not great. Doombolt is weak, Gift of Chaos is amusing if not all that useful and Nurgle's Rot is meh against most thing in power armour (OK against hordes I suppose).
So I think Wind of Chaos is where I'll be for now. Of course, if I drop WoC on both Princes that would be a 60 point saving which is almost the cost of an Obliterator...