Yeah, wav sounds with cue points will repeat indefinitely. I use Goldwave too, it's very easy and you can use the trial version indefinitely--tho i would recommend paying the low, one-time fee for registered use and unlimited updates.
If you want to do many .wav files at once, GoldWave may support batch processing--i don't know that it does--, but even if you have to do each file individually, it doesn't take long:
1. open file
2. edit/cue points/edit curpoints
3. if there are any cues, delete them and save.
keep in mind if you edit the original HL files, in order for them to work properly for someone else playing them, you'll have to include the edited waves. As a courtesy to other users, i would recommend using minimod format, or using subfolders, so you don't screw up other maps that user will use with those same wav files... make sense? If you're not using the original HL files, you don't have to worry about this.
There is an alternative to editing the cues too, you can use a mulitmanager to start and then stop the sound when desired, this way, you don't have to worry about including any edited sound files with your map (again, in the case you're editing the HL originals...)