I liked Dancrumb's suggestion of "It was nice chatting/doing business with you". You can also substitute "a pleasure" for the tepid "nice".
Because these are all stock phrases and aren't meant to be taken literally, I don't see what's wrong with saying things like "meeting" or "talking". You both know what you did, so I don't think there's any problem in that context. It's when you talk about what you did to third parties that you need to be careful about what you say you did.
After all, when greeting old friends with something as innocuous as "How's it going?", you don't expect to hear anything more than "Fine, and how's by you?" You don't expect a rant or a jeremiad.
"It's nice to make your acquaintance" is also good, but it's quite formal. Sometimes, though, it's necessary to be formal. But you don't want to come across as the wrong kind of stiff and rigid.