there is no way to put secondary name node on a separate node if you use HMC to install HDP.
This will be just wasting of the resources, as secondary name node doing almost nothing, just grab editlog from the NameNode and merge it with FS image once in a while. All other times it sitting tight and doing nothing.
As of ganglia and nagios, you can put it on any node in the cluster (you can select the node on the services selection page).
Please, be more specific with puppet kick failure you mention. What is the error message? what logs saying about this? etc…