I have a CS degree and my university also provided a SE degree. The first years, we all studied together. Only in the final year did we study courses that deviated (some were still shared). The final year was about focusing on either the science or the engineering disciples. I felt like it worked really well. The SE's left with a really good knowledge of computational science, while also learning how to engineer solutions. The CS students got some experience in engineering, without it being the main focus.