The decision you are talking about is acceptable and we have seen systems successfully working this way. Most probably everything is going to be all right but there is at list one issue you'd better consider before making a decision. The thing is that to work properly dongle has to have a good response time. Therefore we usually recommend do NOT plug it into any working server (1C, DBMS and so on) which can be a subject to heavy workload and can have not enough resources to provide quick access to dongle.
The much better way is to use a separate computer (not necessarily the server - workstation is enough) which only duty is to serve as "dongle server". When you use virtual environment you basically have no way to guaranty that dongle will response fast enough when there is a heavy workload.
So if there is any possibility to allocate a stand-alone physical computer inside the same network - it's a better choice.