You are correct. Only one Apple ID can be used at a time.
The iMessage protocol was added to Messages (formally iChat) to facilitate the ability to do iPhone-to-computer communication. This was done to allow messages that you would only be able to receive on your iPhone to now be received on your computer and visa versa. Since computers aren't identified by phone number, Apple IDs are used instead. The Apple ID is really only a way of tying a phone number to something that can be used to uniquely identify a computrer. You don't even need to give people your Apple ID for them to contact you using Messages they only need to know your phone number. Apple's servers will take care of tying the phone number to the Apple ID.
I see your point, but when I *send* a message to a phone with Messages, it sends them *from* the email address associated with my Apple ID, without giving me a choice. (The email address appears with the message on the destination phone.) This means I must expose my personal email address to business associates, or vice versa. So it's more than just phone numbers: email addresses are being sent too.
I see, now I understand your delemma. It's the 'caller ID' sent back to the sending party as configured on the iPhone and subsequently in Messages.
Being able to configure two Apple IDs wouldn't solve that problem either since you wouldn't be able to configure Messages to send back the proper caller ID based on who sent the message anyway. That would be a configuration nightmare. The proper thing for Apple to do is to send the 'real name' associated with an Apple ID instead. That way you can configure all your Apple IDs to use your one real name and send that back as the caller ID.