Seconding the Desert Inn on Harbor, not to be confused with the Desert Palms. The Desert Inn has multiple suite options, with the suite C2 being a multi-room setup with 2 queen beds in each, and a little seating area when you walk in. Best Western Plus Anaheim Inn on Harbor also has a limited number of multi-room suites. You can also look into the Tropicana Inn Park View Suites. There's not 2 bedrooms, but 2 separate rooms with one having a pull out couch. Another potential option is the Best Western Park Place Inn & Mini Suites on Harbor. I once did a stay with 3 family's here in 3 different rooms next to each other, 2 of them with adjoining doors. There might be even better options further down Harbor, but I always recommend staying closer to the DL entrance.
It is worth noting that the pools at each of these properties are nothing to write home about. If the pool is important, these hotels are not the right choice. I'd look into multiple rooms with adjoining doors as others have noted.