This has ALWAYS bothered me! Specters are only afraid of one thing: the subtle knife. Because of this, it seems only logical that the subtle knife can kill or damage specters. So if Will is in possession of the only thing in the universe that can kill or damage specters, he could theoretically devote his life to hunting and killing specters thereby making up for the approximately 7 or 8 specters he could expect to create by cutting holes so he could see Lyra. Additionally, it is stated that feelings like love and passion create Dust, and Will and Lyra being together would surely create enough dust to make up for whatever dust would escape into the void during the few seconds it took them to climb through the hole in the universe.
However, I don’t think this is a mistake on behalf of Philip Pullman.
I think that Will and Lyra care so much about the Republic of Heaven, Dust and the fabric of the universe that the idea of damaging those things, even just a little, for their own selfish gain seems repugnant to them; especially to Will.
Keep in mind also that Will’s mother’s mental illness was created by specters, so to him, creating more specters to see Lyra might seem especially unconscionable.
The fact that they made a sacrifice that was so great to avoid doing such a small amount of damage speaks to the morality that they developed throughout the series. (for example, do you think Lyra would have made such a sacrifice at the beginning of The Golden Compass?)
I think that the magnitude of their sacrifice in comparison to the minimal amount of damage that they would have done by allowing themselves to see each other is part of what makes their parting so unbearably sad.