I deleted Dawnguard until I am ready to play through it with my new character, a Companion Werewolf.

Will the people I feed off of now carry over to Dawnguard or not?

They only count if you have Dawnguard installed.

How would it keep track of something it has no knowledge of?

I believe it's tracked in the stats.

Dawnguard plug-in can look in the stats, see how many times I fed, and give me the appropriate perk points.