For New Vegas Script Extender, Steam hasn't been an insurmountable problem. I have a vague recollection that the extender team had some assistance from Valve with the integration, but I may be misremembering. Either way, just because the problems were avoided for New Vegas doesn't mean they'd be avoided for Skyrim.
Of course we have no idea if it will be possible for a script extender to be developed for Skyrim, if it will be necessary, or if the brilliant Script Extender team will want to make one. With all the engine changes it might be a case of starting over from scratch.
Steam worked with the Modders to make xxSE and other modding tools work for Oblivion and Fallout 3. It is not of questionable legality as it is a modding tool for the game and we all know that Bethesda likes people to mod their games. If there was any doubt about that, we would be closing all threads that talk about these tools in the Mods section like we do when mods that are illegal (usually content from other games is used on those) Whether or not we will need Script Extensions remains to be seen.
As some folks know, I am no fan of Steam. However I do not hate Steam either. It is a competent digital distribution tool for games and updates. As far as Anti Piracy goes, I abhor DRM, and Disk Checks bug me as I hate swapping disks to play different games. Steam at least is the least obtrusive DRM scheme that I have come across. I would say that it even gets the game started up faster as it takes so long for the Optical drives to wake up, spool up, read the disk, then let the game launch.
So, I will accept Steam if that is the path they follow, and I will accept a Disk check if that is the path that they follow.