I have applied an isolation coat to an acrylic painting using Soft Gel (semi-gloss). This time it didn't dry clear (possibly not thinned enough and/or overbrushed?) but a milky white in some area. Is this material indeed non-removable, or is there something I can do short of painting over these areas?
First of all, you should be using the Soft Gel Gloss as it has much better clarity. This may be part of the cloudiness you are seeing.

Secondly, sometimes the clarity can take a while depending on the temperature and humidity, so you may wish to observe the work for another day or two. Third, if you didn't mix at least a 2:1 (gel to water), the gel is much more susceptible to holding foam when brushed, especially if the gel is overworked or applied over a textural surface. The added water allows the foam bubbles to rise and pop instead of being trapped in the film.

You're correct with your thoughts about the permanency. There is nothing you can apply to remove just the isolation coat that will not alter the underlying artwork. Depending on the nature of the piece, you may be able to carefully sand down through the Soft Gel, but beyond that, painting over may be much easier and faster.