I\'m using Domain driven N-layered application architecture with EF code first
in my recent project, I defined my Repository
contracts, In Domain
Perhaps using the command-query separation (at the application level) might help a bit.
You should make your repositories dependent on entities only, and keep only the trivial retrieve method - that is, GetOrderById() - on your repository (along with create / update / merge / delete, of course). Imagine that the entities, the repositories, the domain services, the user-interface commands, the application services that handles those commands (for example, a certain web controller that handles POST requests in a web application etc.) represents your write model, the write-side of your application.
Then build a separate read model that could be as dirty as you wish - put there the joins of 5 tables, the code that reads from a file the number of stars in the Universe, multiplies it with the number of books starting with A (after doing a query against Amazon) and builds up a n-dimensional structure that etc. - you get the idea :) But, on the read-model, do not add any code that deals with modifying your entities. You are free to return any View-Models you want from this read model, but do trigger any data changes from here.
The separation of reads and writes should decrease the complexity of the program and make everything a bit more manageable. And you may also see that it won't break the design rules you have mentioned in your question (hopefully).
From a performance point of view, using a read model, that is, writing the code that reads data separately from the code that writes / changes data is as best as you can get :) This is because you can even mangle some SQL code there without sleeping bad at night - and SQL queries, if written well, will give your application a considerable speed boost.
Nota bene: I was joking a bit on what and how you can code your read side - the read-side code should be as clean and simple as the write-side code, of course :)
Furthermore, you may get rid of the generic repository interface if you want, as it just clutters the domain you are modeling and forces every concrete repository to expose methods that are not necessary :) See this. For example, it is highly probable that the Delete() method would never be used for the OrderRepository - as, perhaps, Orders should never be deleted (of course, as always, it depends). Of course you can keep the database-row-managing primitives in a single module and reuse those primitives in your concrete repositories, but to not expose those primitives to anyone else but the implementation of the repositories - simply because they are not needed anywhere else and may confuse a drunk programmer if publicly exposed.
Finally, perhaps it would be also beneficial to not think about Domain Layer, Application Layer, Data Layer or View Models Layer in a too strict manner. Please read this. Packaging your software modules by their real-world meaning / purpose (or feature) is a bit better than packaging them based on an unnatural, hard-to-understand, hard-to-explain-to-a-5-old-kid criterion, that is, packaging them by layer.