Even getting XCode for our own use to put on our Mac build server will be difficult now; $4.99 may be a token price, but any price in the academic world means that things have to get charged against a cost centre; policies mean it probably can't be charged as IT overhead (like Mac build servers and operating systems can) because it is specifically for development, so it needs to be justified as part of a grant. For things like that, the University will probably want Apple to go a months long process to become a designated approver (Apple hardware is not normally purchased direct from Apple), and to pay for things like that by purchase order - the administrative cost of which would be greatly more than $4.99.
The end result of all this is that Apple will probably not be a supported platform for our software any more, and users will be asked to use a virtual machine or move to a different platform if they want to use our software.
Apple is already one of the most difficult platforms to develop on, largely because of the way their linker and object loaders work; it is one of the few platforms (I think Irix is another) where objects to be opened with a dlopen like mechanism are in a different format to normal shared objects; making the barriers higher for academic users trying to develop multi-platform software will simply result in academic and other free software being less available on Mac; some academic users like being on Mac, but I expect that as it becomes progressively more of a disadvantage and Apple becomes more of a pariah, this will change.