One of the meanings of Yisrael is that it is a contraction of the words yashar (straight) and G-dâ€™s name, kEl. I once heard this explained in the name of Rabbi Rosenberg zâ€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 vâ€™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 oneâ€™s family life. But somewhat aside from that, when fulfilled properly, kibud av vâ€™eim, is actually a great means to succeed in oneâ€™s internal journey toward Torah observance. When there is a lack of feeling of kavod (honor) for an individualâ€™s parents, it is impossible that they will be able to proceed through emotional challenges of the tâ€™shuvah process and develop a healthy sense of belonging in the Frum world. (I donâ€™t mean a failure to uphold the halachos in the Shulchan Aruch, but rather a feeling of disdain for oneâ€™s upbringing or lack of gratitude to oneâ€™s parents.)
There are certainly some cases where a baal tâ€™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 tâ€™shuvah can find many examples of Torah values, and middos tovos (good character traits) that they gained in their parentâ€™s home. The goal is to look at the tâ€™shuvah process as building on those positive lessons, rather than replacing those lessons.
A failure to approach tâ€™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 tâ€™shuvah yeshivos and seminaries keep this idea in mind when guiding students. But where they fail to do so, the baalei tâ€™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.