Perl is a very supple language, but it has its quirks. For instance, it isn't at all obvious that scalar keys %$some_hash returns the number of hash elements in constant time. (We had quite a thread on that one, complete with BrowserUK benchmarking). Nor is it obvious that die; (without any parameters) rethrows an exception.
Somebody thought that $#some_array was an intuitive way of specifying the last index of an array, but it wasn't me. Nor do I think scalar @some_array is a particularly obvious way of saying "I want the size of the array". I could come up with quite a list of these oddities.
So perhaps the starting point is to say, "yes, there are parts that are difficult" and then maybe ask them to explain further. Once someone names specifics it is much easier to say "yeah, but that's bad practice and no longer recommended to new programmers". Or if they are talking about something that is hard but powerful, like regexes, one could say: "yes, that is hard, but it allows so much power in just a few keystrokes". And if they are in fact talking about some of the more arcane syntax, well, just agree, but point out that those are just one small part of a language. Every language has its awkwardness. Why, for example, in Java do I have to declare a whole class using boilerplate code just to have a closure?
The other part of their response "Perl only exists as long as Bio data is in text files" completely misses the point as to why Perl is the tool of choice. It isn't the file format that makes bio data text like - it is the gene sequences themselves. As long as RNA and DNA comes in chains, you will need regexes and as long as Perl is the regex processor of choice, it will have a use.