EF is an ORM. There are many ORMs for dotnet. You can start here:
http://en.wikipedia.org/wiki/List_of_object-relational_mapping_software[
^] (section .net). But you can also google for it, because there are more - many more.
But if you are afraid of any performance issues because of the large table number (might be an architectural mistake on it's own), you can use the plain old approach (SQLCommand and it's friends). Still, I am not sure, that you really gain a lot. EF is really good, and you loose a lot on other scenes of the lifecycle by not using an ORM.
But to choose the best ORM for your needs... well, that could be a challenging task. Performance and complexity are two opposite things. You could place EF and NHybernate on one end and this one for example at the other one:
ServiceStack.OrmLite[
^]. But you have to decide based on your real needs.
My opinion: if you end up with 1000+ tables, you probably should look around in other data store concepts, like
noSQL[
^].