One of the meanings of Yisrael is that it is a contraction of the words yashar (straight) and G-d’s name, kEl. I once heard this explained in the name of Rabbi Rosenberg z”l, the founder of Machon Shlomo, that one can only truly draw close to G-d by traveling in a straight path. This can be accomplished only when one has a clear recognition and appreciation of where they are starting from. Kibud av v’eim (honoring parents) is a mitzvah of great importance and a foundation of the Torah. It is also a good way to minimize friction in one’s family life. But somewhat aside from that, when fulfilled properly, kibud av v’eim, is actually a great means to succeed in one’s internal journey toward Torah observance. When there is a lack of feeling of kavod (honor) for an individual’s parents, it is impossible that they will be able to proceed through emotional challenges of the t’shuvah process and develop a healthy sense of belonging in the Frum world. (I don’t mean a failure to uphold the halachos in the Shulchan Aruch, but rather a feeling of disdain for one’s upbringing or lack of gratitude to one’s parents.)
There are certainly some cases where a baal t’shuvah grew up with abusive parents. In which case, they need to seek guidance from a Rav with experience in these issues and / or a counselor. However, in the vast majority of cases, the baal t’shuvah can find many examples of Torah values, and middos tovos (good character traits) that they gained in their parent’s home. The goal is to look at the t’shuvah process as building on those positive lessons, rather than replacing those lessons.
A failure to approach t’shuvah as a continuation of the positive can cause personal confusion and loss of sense of self. It is critical, in my opinion, that the baalei t’shuvah yeshivos and seminaries keep this idea in mind when guiding students. But where they fail to do so, the baalei t’shuvah themselves should keep it in mind. For example, a young man comes to yeshiva. His parents instilled in him the great importance of self-sufficiency and hard work. His rebbeim see that he is extremely talented in learning Gemora. They want to steer him toward a Kollel life-style. They explain that Torah study maintains the existence of the world, and that it is much more important than any other occupation. They build up his belief in his own abilities as a potential Torah scholar. In doing so they, may be undermining a critical pillar of his self-esteem (which is also an important Torah value) and it may be years later until her manages to get back on track.
The example is very simplistic and every case requires its own consideration. But, as a general rule, one needs to find consistency in their past, present and future.