I'm using guile in for configuring a "real time" application (a sort of network sniffer) as well as offering some kind of live introspection of the internals of the program. This program is not allowed to stop working during garbage collection either.
With Guile 1.8, only the guile threads are stopped during the GC, so the other C threads that perform the actual work are not at all affected by this, assuming they do not enter guile mode frequently/at all. It is my understanding that it's the same with the new GC used in guile 2.0.