it would run continuously but compressors are rated for continuous duty.. personally id fix the Transair.. if you go back to just the dash air and its not a completely separate system.. ie is a tie-in with the trans / air then you;ll have to buiy a bunch of parts anyway... may as well fix the trans/air.. not sure what you mean by "worn".. are the hoses rubbed through? coils corroded and leaking? or is it just relays, circuit breakers and bad fan motors.. and in need of a good cleaning?
usually burnt up compressors are a result iof malfunctioning condensers.. either overcharged freon, bad fans, clogged coils..
ive had my red bus and my dev bus on LONG trips in summer where I know the compressors ran from noon till dark never cycling out... all those compressors are still in there years later.... as long as the system works properly, is charged with refrigerant OIL properly the compressor can run for long periods no worries...