Saladin, Les Moonves wants you to buy everything, in as many forms as his people can release it.
And what would have been the dramatic point of including Sisko's appearance in "Emissary", if you didn't also create new footage of other captains on other ships at Wolf 359? A short series of cameos—in a scene that this two-parter deliberately did not show—just so continuity nerds could feel the attention. There'd be no follow-up, and it'd look like a fan edit.
Zefno, switching DVDs isn't that hard. Really.
I'm not a huge fan of re-editing Trek episodes to fake the appearance of one continuous work, unless it's possibly to add footage that had to be trimmed for broadcast. This rarely happens, because those kinds of cuts were usually made before post-production, and fixing things like sound is rarely in the budget for the home release of a tv series.
I'd rather keep to the rhythm of the original two-parters where possible. All you'd really need to do is delete the "to be continued" title at the end of most Part Ones, especially if the rest of the presentation is keeping Act breaks intact.