Some people have had there Macs running folding programs 24/7 for long periods of time with no problems. Those things consume 100% CPU all the time. The fans SCREAM!
I run my MacBook Pro 24/7 and it still runs perfectly after almost a year now. I rarely if ever shut it off and my processor usage is similar to that of playing music.
Leave it on if ya want. No harm to them. Infact the less your hard drive has to power up the less strain on it I think? Plus don't worry about heat. The fans control that and it will be sitting on a desk I presume?