I Have Been suffering from same thing since long time. It specially happens when you're connected to remote server(Which might be slow), or you have poor network connection.
I doubt if Microsoft knows what the right answer is.
But since I've tried to find the solution. Only 1 layman approach worked
- Click the close button over the tab of query which you are being suffered of.
After a while (If Microsoft is not harsh on you !!!) you might get a window asking this
"The query is currently executing. Do you want to cancel the query?"
And post that, may be you're studio is stable again to execute your query.
What it does in background is disconnecting your query window with the connection. So for running the query again, it will take time for connecting the remote server again. But trust me this trade-off is far better than the suffering of seeing that timer which runs for eternity.
PS: This works for me, Kudos if works for you too. !!!