Red button, or blue button?

Either way, the ultimate outcome is the same, as

The machine was going to be activated anyway, whether by you or them. He himself says he would have activated it anyway had you pressed either button.

There doesn't appear to be any difference in the later game based on your choice.

Red button - activates it Blue button - Deactivates but scientist still activates it

Bummer indeed, but yeah either way the thing still gets activated and you will still have to chase to stop it.

The Blue button shuts it down and the Red one activates it, but either way it gets activated, you'll see.