If you only have the one base, the recharge time on the widow mine is quite significant. You could, in theory, send your SCVs back to mine, and then pull them away before the rearm time is complete, and then send a marine or other expendable unit to trigger the mine. This is very risky, but if you're timing is correct, you will take even less economic damage than having them not mining at all.
The more cautious route in a case like this, is to definitely move your workers away. The economic loss that you take from losing workers to dying and then having to rebuild them is significantly more than the lost mining time while waiting for enough energy to scan. You always want to keep workers alive in Starcraft 2. They are the backbone of your chances of winning.
Instead of lifting off and moving, I would consider just sending the SCVs to simply mine from the mineral patches at the nearest base and then after the mines are killed, send them back to mine from the original mineral patches. The return path from the other mineral patches will leave your SCVs out of range of the Widow Mines.