I think the biggest worry with many studios is probably the reverse-engineering aspect of modding rather than anything the modders might do.
A large part of the press may be utterly ignorant and disinclined to check their facts, but I've yet to hear of any adverse PR created by a genuine game mod. I certainly don't blame any company that wants to protect the secrets of its game engine, though - which is the livelihood of that company, after all.
