Because he didn't realize how truly far gone Anakin was at that point.
Other than that, I can understand the sentiment of these. Sure, it's really easy to go on a message board and discuss these issues ad nauseum until someone makes sense of them (either through screenplays, interviews, or EU), but on their own, there's a lot of information that just falls through cracks to the casual viewer (i.e. kids.)
I'm not going to force my kids to watch it one way or another - although, I've not played it myself in some time. At some point, I'm probably going to make a no-frills transfer of the X0 cap and use that for casual viewing, so unless my kids ask me to put the PT in, it'll probably stay on the shelf (though I've not gotten ROTS yet, but for the record, my daughter did not enjoy watching it in the theater.)