The indictment charges Assange with conspiring with Manning to unlawfully gain new access to a protected government computer system. Specifically:
* Assange gave Manning a CD to boot from on the target computer, containing tools to copy the protected password data.
* Assange received a copy of the password hashes from Manning, and attempted to crack them.
Regardless of what reasons the Obama administration had to proceed or not proceed with the indictment at the time (which we are not privy to), these are very clearly defined criminal offenses in the USA, with much precedent behind them. Had Assange not provided the hacking tools, and had he not attempted to crack the passwords, this indictment would never have happened.
Press freedom and protecting your sources is not the issue here; it's about conspiring to hack a government computer.
[1] https://www.lawfareblog.com/document-julian-assange-indictme...