I would say to finish out the cycle. You may be subconsciously stressing about it and waking yourself up. Once you have been doing this a while it might not be so stressful and you might start sleeping better again. Kind of like if you are stressing about something important the next day and keep waking up thinking your going to be late or sleep through your alarm clock or something... KWIM??
You might also find that the frequent waking doesn't matter much. I started temping again when my DS was still waking frequently through the night, and once he started to sleep through the night, I kept waking waiting for HIM to wake... Anyway, I noticed that it didn't matter much what time I took my temp and I just took my temp whenever I woke up and each time I woke up and saved the one I thought was probably most accurate.

Good luck!
Oh, and I've also noticed that my temps get pretty erradic the first week or so of my cycle, then start to even out closer to O.