He basically had to keep up the charade
It was essential to the rebels' plan that the Capitol not realize anything was up until right when the force field was destroyed. Accordingly, they crafted a plausible story for why Beetee would be messing around the lightning tree with a spool of highly conductive wires. If Beetee had told Katniss and Johanna to stay, it would have immediately indicated that he didn't actually plan on electrocuting the other Tributes, making the Capitol suspicious.
Also, Katniss and Peeta were intentionally kept in the dark. There would have been no way of telling them that the plan was off without immediately arousing their suspicions. At this point, they were both planning on abandoning the group once the Careers were dead. Acting suspiciously could have potentially fractured the group, making rescue that much more difficult.
So someone had to set up the wire. Peeta and Katniss needed to be protected from the Careers, so he couldn't send both of them or keep them both at the tree. So he split them up so that Finnick and Johanna could each protect one of them. Peeta was weakened from his encounter with the force field, so sending Katniss and a protector made the most sense.