I quite agree with you, but not completely. It's true that Turing & Cburch fundamentals are complete, in that anything we describe in computation can be expressed in terms of those. But I think we are using a very small subset of all Turing-Church based computing, and refinements of this understanding will provide a qualitatively better algebra for the types of software we really create. This will make it easier both for engineers to create software, and for end-users to do things that nowadays only programmers can do.

Both ends you describe (computer science and software engineering) are to me part of the same continuum. We still have articulate most of it with a coherent theory.