Generative Artificial Intelligence (GAI) can be seen as a double-edged weapon in education. Indeed, it may provide personalized, interactive and empowering pedagogical sequences that could favor students' intrinsic motivation, active engagement and help them have more control over their learning. But at the same time, other GAI properties such as the lack of uncertainty signalling even in cases of failure (particularly with Large Language Models (LLMs)) could lead to opposite effects, e.g. over-estimation of one's own competencies, passiveness, loss of curious and critical-thinking sense, etc.These negative effects are due in particular to the lack of a pedagogical stance in these models' behaviors. Indeed, as opposed to standard pedagogical activities, GAI systems are often designed to answers users' inquiries easily and conveniently, without asking them to make an effort, and without focusing on their learning process and/or outcomes.This article starts by outlining some of these opportunities and challenges surrounding the use of GAI in education, with a focus on the effects on students' active learning strategies and related metacognitive skills. Then, we present a framework for introducing pedagogical transparency in GAI-based educational applications. This framework presents 1) training methods to include pedagogical principles in the models, 2) methods to ensure controlled and pedagogically-relevant interactions when designing activities with GAI and 3) educational methods enabling students to acquire the relevant skills to properly benefit from the use of GAI in their learning activities (meta-cognitive skills, GAI litteracy).