The reason why Paul had to deal with them was because they were killing associates of the Gambinos ie Ruby Stein and Paul didn't want anymore unsanctioned hits since there was a lot of money at stake (and we all know how much Paul loved his dollars)

And seeing they were considered cowboys- it was probably felt nobody other than the boss himself could get thru to them/ control them and that's exactly what the Gambino's did. To show them force