No permission is needed to credit, cite or link to Project Gutenberg as the source of something you use. This applies even for commercial use.
Firstly, I think you may have misunderstood this a bit. The text isn't saying you shouldn't cite Project Gutenberg; in fact, it's saying the opposite -- that you don't need permission to cite them.
Project Gutenberg even has explicit instructions for how you can cite them here. They give an example:
Carroll, Lewis. (2006). Alice in Wonderland. Urbana, Illinois: Project Gutenberg. Retrieved February 21, 2016, from www.gutenberg.org/ebooks/19033.
The above assumes that Project Gutenberg is the publisher for the version you are citing. That seems valid enough to me, as many books are published in various versions anyway, and you would just be citing one of those versions. The most important thing is not the publisher, but the author and title of the work -- the rest, including the year, is just there so that someone else can find the book that you were reading.
Here is a related question about 2nd editions of books. Note the advice there: You cite the version of the text that you read, not a version that you didn't read. The problem is the quote, page number, etc. may differ in different versions, so you want to be careful. I see Project Gutenberg as an online version of a previously in-print book.
However, some caveats:
It is confusing that the year will be off if you cite Project Gutenberg, so it would always be good to include a parenthetical in the citation: e.g.
(originally published 1865) for Alice in Wonderland.
Be aware that citing Project Gutenberg is a bit nontraditional; probably most people would prefer to cite a print version. But that culture may be changing, and I don't see anything particularly wrong with citing the version that you read.
If you prefer to be safe, you can choose to instead cite a print book, e.g. using an ISBN found on Amazon. In this case, if you wish to credit Project Gutenberg for their help, you can include something in the acknowledgements to your article:
Acknowledgements. The authors would like to thank Project Gutenberg for making some books referenced in this article available online.