use of pre-empt

Solution 1:

Both "pre-empt" and "counter" imply opposition to the foreseen event. I suggest "anticipate" instead:

I want someone to start in May, but as the Indian summer is May / June, I want to anticipate the possibility that one of them will be on leave then, so I am sending two proposals.

Solution 2:

At a stretch, preempt ("to appropriate something (before someone else does)" or "to displace something, or take precedence over something") can be used as you suggest, but I'd prefer preclude ("remove the possibility of; rule out; prevent or exclude; to make impossible") or forestall ("to prevent, delay or hinder something by taking precautionary or anticipatory measures; to avert" or "to preclude or bar from happening, render impossible"), or decrease, limit, etc. depending on your purpose and the intensity with which you propose to counter the possibility. More colloquially, consider scotch, stymie, and stave off.

Solution 3:

If you know something is likely to happen, you can try to circumvent it:

: to manage to get around especially by ingenuity or stratagem

So you could write:

I want someone to start in May, but as the Indian summer is May / June, I want to circumvent the possibility that one of them will be on leave then, so I am sending two proposals.