Great question! Cognitive activation seems to be key for learning, but how can one measure mental processes and not use the products. From the literature I know, I see three options:
1. define and observe valid behavioral criteria, based on empirical research, such as they are listed in the Orientierungsrahmen Unterrichtsqualität, section 10, or use observed time-on-Task (Helmke & Renkl, 1992, 1993; Münchner Aufmerksamkeitsinventar)
2. use Student self-report of mental activity, as in the Paas-Scale or in Krell's questionnaire:
Krell, M. (2015). Evaluating an instrument to measure mental load and mental effort using Item Response Theory. Research Letters, 1-6.
Paas, Fred GWC, and Jeroen JG Van Merriënboer. "The efficiency of instructional conditions: An approach to combine mental effort and performance measures." Human Factors: The Journal of the Human Factors and Ergonomics Society 35.4 (1993): 737-743.
3. use think-aloud techniques to describe degrees of complexity in student explanations (see attached papers).
Let me know how you did it and what your experience is.