i think you r misunderstanding something here. the positive charge was discovered by then.. because they knew electric fields by that time..
i think this question came into your mind when speculating about the gold foil experiment i guess?
well im not 100% sure.. but according to my knowledge and the stuff i read to answer ur question, it is a matter of the exact times of those discoveries...
micheal faraday who was famous for stuff regarding electricity was there before rutherford.. so i guess u agree with me for saying that ppl at that time knew about electric fields and how to differ positive and negative charged particles.
according to this article, before rutherford proved that alpha rays were actually particles, the idea was there about alphas being a fast moving positively charged ion of atomic mass, which made rutherford to look into the matter more thoroughly.
i suggest u read the "II. Alpha as a Particle Happens in 1903" of the above article