I have a custom button on a sales order. After it is clicked, how can I disable it to prevent multiple clicks?

Create the button in a workflow and have that trigger the next event. It will natively ask you if you really want to submit the data again with a popup

Can't unfortunately. I need this to be scripted as it's a little special

Gotcha. I had this same issue and I converted it to a workflow with a workflow action script that passed the logic the same way as the previous way.