Odds are that the threadless stem hasn't harmed the fork yet, since the usual harm is a fracture. You also will be cutting off much of the extended height, where the damage would have occurred (if any did), and anyway the quill will buttress the fork to beyond the thread depth, so strength won't be an issue.

But there are a few wrinkles to check on before going forward.

1- you need thread extending to below the bottom of the top bearing. As a rough guide, that means that the unthreaded section needs to be no longer than about 15mm longer than the head tube. That allows for the height of the lower bearing plus a bit of wiggle room.

2- the thread has to extend no deeper than 2-1/2" below the top of the headset, so the quill stem will end at least 1/2" below the last thread (1" is better), more than that doesn't make a difference.

You'll also need to cut the fork, which is easy enough, but measure carefully, and thread on the top bearing first so you can roll out the cutting bur on the new first thread. Threaded forks need straighter cuts than unhreaded, so either use an old steel top cup as a guide, or put a hose clamp around the fork as a cutting guide. Don't measure the fork for a super close fit on the headset, but instead allow a few millimeters for a spacer. Headsets vary in stack height and one day that extra bit of length can become very important.

Before starting, I'd drop the fork, and measure it against the head tube to see if it fits conditions 1 and 2. I suspect, that thread length may be an issue, which might explain why the prior owner went threadless. If so, the threads can be extended by a skilled shop, but figure it'll cost you about $20-25.

If the thread length means you're stuck with this hybrid arrangement, come back and I'll give you pointers on how it can be made safe.