So what's it going to do to the honey? Will we have spider venom laced honey?

As article suggest - it is fully biodegradable. I suppose venom has some short half-life. And since peptide is isolated, not full chain toxin, it should be harmless to humans.

I'd imagine eating it has a different effect than having it directly enter the bloodstream as well.

Seems reasonable. After all, spicy ramen is probably also more dangerous when introduced directly to the bloodstream. ;)

A lot of people might become allergic to honey, and never know why.

Probably, but not at any meaningful concentration.