I think Atlassian is indeed acquiring Trello to fit it in with the rest of their suite. This is probably going to be done to the detriment of the other use cases.
On the bright side, this might pave the way for a new product in this space, or some open-source tools which replicate the same basic funtionality.
Open source alternatives are already out there. Wekan is one of the more popular ones. I'm not sure if it has all of the features of Trello as I haven't used Trello extensively.
https://github.com/wekan/wekan
Looking at the screenshot it looks more like a ripoff than an alternative. I am an open source advocate in almost everything, but that kind of ripping of / stealing ideas leave a bad taste.
On the bright side, this might pave the way for a new product in this space, or some open-source tools which replicate the same basic funtionality.