Um no it's not okay, you're skewing the results. (I'm not sure how you come to the conclusion that you're NOT skewing them, to be honest.) Heads and tails should have an equal chance to show up, <= 0.5 means that one has a higher chance of showing than the other, which is inaccurate. It's pretty basic maths. For it to be even you'd need:
0.0000 - 0.4999 = heads
0.5000 - 0.9999 = tails
This way, each side has 5000 possible ways to win, instead of your suggested approach which would give heads 5001 ways to win and tails 4999 ways to win. 5001/4999 != 50/50.