For the moment my solution to this problem was incorporating two .svc files in my webservice to separate the two interfaces. Such, I have localhost/WebServiceName/Service1.svc and localhost/WebServiceName/Service2.svc.
With the endpoint configuration
<services>
<service behaviorConfiguration="WebServiceName.ServiceBehavior1" name="WebServiceName.Service1">
<endpoint address="" binding="wsHttpBinding" bindingConfiguration="Binding1"
contract="WebServiceName.I_Service1" />
<endpoint address="mex" binding="mexHttpBinding" contract="IMetadataExchange" />
<host>
<baseAddresses>
<add baseAddress="http://localhost/WebServiceName/Service1.svc" />
</baseAddresses>
</host>
</service>
<service behaviorConfiguration="WebServiceName.ServiceBehavior2" name="WebServiceName.Service2">
<endpoint address="" binding="wsHttpBinding" bindingConfiguration="Binding2"
contract="WebServiceName.I_Service2" />
<endpoint address="mex" binding="mexHttpBinding" contract="IMetadataExchange" />
<host>
<baseAddresses>
<add baseAddress="http://localhost/WebServiceName/Service1.svc" />
</baseAddresses>
</host>
</service>
</services>
This solution is not necessary the best one (if a client really wants, it can find that this service exposes 2 different interfaces, but I can secure them with different credentials/tokens). But at the moment I will go with it.