Metaphors are a great way to explain a concept. If anything you are expanding their thinking abilities. Metaphors stimulate deeper, more meaningful learning and just education that can be regurgitated. They work on many levels because they help all types of learners: visual, audio/verbal, tactile, and kinesthetic.
The power of metaphors is profound. For example, I am going to use metaphor as a means to convey a learning model I am developing for my dissertation. If you run across any naysayers, there is plenty of research and even books about the power and usefulness of using metaphors. If you want some researcher names, feel free to contact me!
And most of science is based on metaphors. Think about how atoms were first described using the plum pudding model and analogy (but I guess you already know that). So, keep at it with the metaphors and even encourage your students to come up with their own and share them with the class. You could even have a friendly contest for the best one created. Then you could even do a cross-class comparison.