Yes. Every company I've worked for that had established (read not startups/not tiny) companies as customers could never use any thing like this due to contracts saying we won't be storing/transmitting their "stuff" on servers we do not control. [everyone hand waves email delivery but we can't use something like gmail].
These are tools for small / startup companies were you need something to just work and don't have resources to spend on anything but getting "established".
They have a behind the firewall version of hipchat for security concious corp customers.
That's pretty much what happened with us. We ended up rolling our own thing and deploying it on our VPN with LDAP authentication: https://github.com/sdelements/lets-chat
It's been working pretty nicely.
They do offer an internal hipchat server as a beta: https://www.hipchat.com/server Not total confidentiality but better.