I don't see a problem with people expressing their frustration. A species that was universally adored on this forum and is really hard to come by is gone. In its place is a species that most of us have seen too many times to count. It is, for most of us, a big downgrade. We are allowed to feel upset, and we are allowed to discuss with other people online why we feel upset.
In the past I have found myself infuriated at people's irrational (or so I deemed it) criticism of ZSL. But I don't think this is irrational. I'm sure ZSL have their reasons not to replace the old hippos with new ones, but they haven't told us this. Most of us were very disappointed to see the hippos had left - a species that is charismatic and crowd-pleasing, yet also extremely rare in captivity in this country. A joy for casual zoo-goers and enthusiasts alike, as well as a species that has played a huge role in the Society's long and fascinating history. It was sad that they are gone, but I think most of us, including me, took a similar approach of hoping that whatever replaced them was similarly amazing and gave us enough of a 'silver lining' to move on from the hippos. For most of us (and I am glad to hear that there are exceptions who love the species), capybara just don't cut it.
I adore ZSL, and I adore the very much upwards trajectory that the zoo is on at the moment. But that doesn't mean they aren't open to criticism. No-one is. My football club is currently in the best place it has ever been under the best manager that it has ever had, but if he makes a poor substitution that costs us the game, I will criticise him all the same. That analogy applies here, I think. With the rate at which new, interesting species are arriving and that new, high-quality exhibits are closing, ZSL is arguably at the best place it has been in years, and I love that. But I still criticise them where I deem it warranted.
Other people will be better-informed on this than myself, but I don't think people at ZSL (or any other zoo) in power to make decisions such as this typically read through these forums. And if they do so, then they can either conclude that us enthusiasts make up a small percentage of their visitor numbers and dismiss it, or interpret it as constructive criticism from people who are really passionate about it. I don't believe there is any damage done to the zoo or anyone else by being a bit critical, as long as it isn't excessive, unfair, or targetted at particular staff members. Therefore, I don't see a problem with people continuing to point out any disappointments with our beloved zoos, and I will continue to do so. So long as nobody is doing it 'for the sake of it,' irrationally or unfairly.
As a side-note, I am delighted to hear that the keepers at Whipsnade don't share our sadness and are looking forward to working with the species.

It is very important that the staff enjoy their work and don't look back on the days of working with hippos too regretfully. Asides from my personal bias that comes from having just seen them too many times, capybara are cute, interesting, and potentially fun to work with.