I like that comeback. Often people will come back with, gravity is also only a theory.Very true.
And the distinction between objectively observable facts (like the effects of gravity, or the fact that life has changed over time and is changing around us today) and the theories that explain them is one thing that many people absolutely refuse* to understand, no matter how thoroughly and eloquently various scientists have been trying to explain this over the last 30-40 years since the serious move to re-incorporate a particular religious view into government and secular life first re-asserted itself in the US during the late 20th century.
The refusal to accept scientific (or any other kind of) data that is "inconvenient" to one's world view has moved far beyond the so-called religious right, though, and it is now being used by business interests to deny climate change etc. Heck, it's even being used to deny actions and events that are matters of public record.
* I say "refuse" because it's not that hard to understand, but it behooves certain interests to cover their ears and chant, "Lalalala, I can't hear you!"
My snappy comeback when people say that evolution is "only" a theory is to point out that the notion that microbes are responsible for communicable disease is also a theory, but would they want to eat in a restaurant where employees don't wash the dishes or their own hands, and oh by the way, how do they feel about people who don't cover their coughs or about sipping soda from the same can as someone with the flu?
We tend to think of issues like science denial as a knowledge deficit problem. Most of the time it is not a knowledge deficit, rather there are other barriers to said persons figuring out the real world.
It matters how we frame our arguments. If the evolution denier says evolution is only a theory, that person is misusing language to confirm their denial bias. A long explanation about the definition of scientific theory and/or hypotheses will only leave them yawning. I have long argued with my science-based friends not to go that route.
But there is no reason to adopt imprecise language like referring to an evidence-based conclusion as a fact because it will surely come back to bite you on the ass if/when some 'fact' turns out not to be supported by some 'new' evidence.
When it comes to evolution, I often use the framing, 'overwhelming evidence supports evolution theory'.