Of course folksonomies (FK) belong in the corporate environment. The do because they are a very "human" way of organizing data based on importance, and relevance.
In some senses, folksonomies have always existed in the enterprise: water cooler chatter, and conversations at the campus cafeteria have always self selected the topics that humans find most interesting. Say it's 1980. Corporations have lots of info stored in file cabinets. If everyone in a corporation comes across slightly different information, chances are one of them will come across some little-know but useful fact. Could be product info, or some HR policy that is particularly interesting. The person that finds it and thinks it relevant would talk about it with colleagues. The other colleagues at the water cooler would also offer their tidbits of info. If the colleagues agreed that the HR policy topic was interesting, they would repeat it with other colleagues, resulting in a sort of vote/validation driven "rumor mill" type of relevance screen. Eventually, one could see that everyone would get the important information about the HR policy.
But despite the rosy communication picture presented above, there are limitations to how well this can work. The "champion" of the HR policy story could be a lousy story teller, and the topic could die at step 1. The information could get mangled and re-related poorly as it got passed from person to person, to where the "rumor mill" had pretty much ground the original idea up and spit out garbage. (ex: Last week someone told me that UNICEF was against foreign adoptions. I checked it out today, and that wasn't correct. That information had been mangled through the oral tradition. If it weren't' for the Internet, I probably would still be mis-informed.) So despite the fact that we've always had folksonomies, they have been erratic in their performance, and the quality of the shared information has been impaired.
But what if a 2005 corporation formalized all of its information into an electronic library, and made it all available. Sounds great, for sure. Put all the white papers, all the HR forms, all the databases, all the client info, all the competitive data, all the market research, all the pricing info, all the product design docs, all the specs, yada, yada, into a big ol' intranet. Then we could assure that no information got mangled because we'd all have access to the original source. But unfortunately, like the Internet, employees get buried by a mountain of information, which ends up almost as useless as before the information age. Grated, a search can reveal exactly the sought information, but what if someone doesn't know what is worth searching for?
So now, combine the two advancements: the information age's ability to catalog all the information, with the folksonomy's ability to democratically find and assign an interest level on particular pieces of data. All of a sudden, the important, relevant information starts to pop out. People searching for "pricing" of the company's products don't get results from 1997, but they will first get current pricing, because that's what other users have identified as a "hot topic". That obscure HR policy would get "dugg" by the same person who found it in 1980, but instead of just chatting about it at the water cooler, they would tag it as important. Others would see the tag and agree, others would do a search after hearing about it at the cooler and agree, and pretty quickly this topic would trickle up to the top. Soon, everyone at the firm would know about this policy -- with the correct information. Then the relevance would fade a little as the topic got less "hot". To me, that's a beautiful management of "corporate intelligence".
In a sense, that's what Techdirt has done for corporate news for some time with their subscription service. Intelligently find, tag, and show news that is relevant to a company. Instead of having to read all the news every day, corporate customers of Techdirt can rely on intelligent (but centralized) filtering of the news. A folksonomy could easily compete with this service. For example staff could tag any news story they found relevant, and as such each employee would not have to comb the newsworld every day, since the enterprise would develop its own "intelligence" about which stories were relevant to it. Pretty cool. (Oh, but you wouldn't necessarily get the analytical advantage, although you could get some interesting discussion.)
As an answer to "how do you manage and merge folksonomies and existing taxonomies?" I think the answer is a simple one: as an overlay to however you manage your information now. Delicious (I'm not doing the caps thing on that) and Digg are overlays to the net -- seems to work well, no?