In other words, Petraeus could not be seen using those applications. Official secure email goes through official secure channels. Personal email went to through gmail / yahoo / etc.
If someone had found out Petraeus was using a different email app (and I'm sure they would have), it would have immediately raised suspicions as to why the Director of the CIA was using a secure email app that wasn't the gov's official secure email app.
I think the safest thing for Petraeus would have been to only send short coded messages via gmail (e.g. "talk at 10 pm" but replace that text with code words) and then to conduct most of the communication infrequently and in person.
But, clearly, Petraeus wasn't thinking clearly ...
Clearly, Petraeus is a very smart guy, and has accomplished many great things for himself and for his country.
When this started, he probably said to himself "it's just a one time thing ...," but inevitably, it escalated, and he slid down the slippery slope of bad decisions.