At least with Solr 4.6.1, replica are considered as active during the warming process.
This means that if you restart a replica or create a new one, queries will
be send to this replica and the query will hang until the end of the warming
process (If cold searchers are not used).
You cannot add or restart a node silently anymore.
I think that the fact that the replica is active is not a bad thing.
But, the HttpShardHandler and the CloudSolrServer class should take the warming process in account.
Currently, I have developped a new very simple component which check that a searcher is registered.
I am also developping custom HttpShardHandler and CloudSolrServer classes which will check the warming process in addition to the ACTIVE status in the cluster state.
This seems to be more a workaround than a solution but that's all I can do in this version.