A counter should be able to switch into any attack commonly used and either be able to live a second attack and OHKO in return, or outspeed/out-prioritize and OHKO, or else be able to just stall it out effectively. Breloom can do none of those things to Greninja, as it can't switch into an Ice Beam.
Now, if you can get Breloom in for free after the Greninja becomes Ice type, or you can switch in on a predicted Dark Pulse, or if Breloom vs Greninja is the lead matchup (like in your example), you can probably OHKO Greninja with Mach Punch.
So to answer your question in short... technically, no. But it is a decent check.