As someone who quit advertising on reddit because inventories were never available on the subs I was interested in, I can see why you would make this change.
I guess the simple middle ground here is to charge different fee for subscribers vs. subreddits.
Want to target the 17 million subscribers on /r/pics? You have to pay a low fee. But if you have to be seen by one of those 1700 people viewing r/pics right now? Pay higher.
It addresses the concerns of redditors like bold_panda as well as helps maximize inventory utilization.