Generative artificial intelligence (GenAI) is used in programming education; however, its adoption can introduce pedagogical misalignment, shallow cognitive engagement, and ethical risks that threaten the sustenance of programming skills of students. This study evaluated the GenAI programming education framework’s ability to sustain higher-order thinking skills (HOTS) and programming logic while mitigating pedagogical, cognitive, and ethical barriers in Java programming. A between-group mixed-methods experiment was conducted amongst 124 undergraduate students (62 in the control group and 62 in the experimental group) over 7 weeks. Learning outcomes were assessed using pretests and posttests, analyzed with baseline-adjusted ANCOVA and MANCOVA, and supplemented with trace-based learning analytics from GenAI logs collected at time points (Weeks 3 and 7). The experimental group showed a baseline-adjusted advantage on HOTS (adjusted mean difference = 0.29; p < 0.001; adjusted Hedges’ g = 0.80) and a smaller but significant improvement in programming logic (adjusted mean difference = 0.21; p = 0.047; adjusted Hedges’ g = 0.36), alongside a multivariate group effect across domains. Log-derived indices also showed larger gains in pedagogical alignment and cognitive engagement, reflected in more frequent task decomposition and debugging behaviors. Ethical engagement has also increased, indicating consistent hallucination and data sensitivity awareness. Path modelling indicated that the intervention increased changes in pedagogical, cognitive, and ethical engagement. Pedagogical alignment and cognitive engagement were positively associated with post-test HOTS and programming logic, whereas ethical engagement was negatively associated with HOTS but not significantly associated with programming logic. Overall, the findings suggest that GenAI becomes more educationally beneficial in programming when guided by a structured approach.