No. In Jainism, honey is generally not eaten because it involves violence to bees and their colony. Even when the honey is taken without directly killing every bee, the process usually harms living beings and disturbs their life, so it is considered abhakshya in Jain dietary discipline.

So your understanding is correct: honey can harm bees, and that is one reason Jains avoid it.

If you want, I can also explain which foods are considered abhakshya in Jainism.