As long as you are sure you are not going to skill break said ninja, I do believe you can turn his fragments into points without hesitation.

That being said, if you do not care about getting to Iruka right now, you might want to wait with using the medium refining, it may be soon, it may take months, to be honest I have no clue whatsoever when it will be added, but the refining rewards will be boosted in the future.

It's all about how patient you are and how much do you care about such things. Now, I do not remember exact boosts, but for sure it does increase the number of seal scrolls and summoning scrolls you get per refine, as well as add few more potential items.

I have no info about the points being reset when it's added, so as I said I believe you may just turn them into points right now, but if you are worried about that, you can keep them for when the time comes.