I can sympathize with Hershel's decision to lock up the zombies, especially his family. During an initial outbreak I think I'd be more likely to lock up a loved one who was acting that way than I would be to bash their skull in if I had the option. Then, once that's done it might be easier emotionally to simply let them be than to go in and finish them off.

That said, that's not really the reason I said that I didn't think Shane's decision to clean out the barn made sense.

First, it went against the landowner's explicit desires; it simply wasn't Shane's decision to make. If you don't agree with your host and can't come to amicable terms, you leave. Shane, on the other hand, proved to Hershel that the group wasn't trustworthy which will likely result in their being forced to leave anyway.

Second, there was no immediate threat. If the zombies had broke out themselves, I'd likely have a different opinion, but the trapped zombies were pretty much just standing around and there was no evidence that the barn wasn't secure enough to hold them. Again, if you did think the risk was too high the appropriate response would be to discuss the issue with the landowner (like Rick did) and, if unsatisfied, either leave or post your own lookout to ensure your group is safe.

Basically, I can't see any potential upside to the "plan" to clean out the barn - it does nothing but damage the relationship between the host & guests.

The only way I can see it not being a completely horrible idea is if the ultimate plan is to simply take over the farm by force.