It isn't the happy ending that's the issue - in fact, I don't think The Visitor has that happy an ending. Sure, they save Ben, they kind of had to in order to have an episode the next week, but he remembers watching his son's life become about grief and obsession and tragedy in his absence, something which tied in to all the long build up of Sisko as a single parent. Sisko's embrace of Jake has so much subtext. It's quite bittersweet.
The issue here is the ending has no earned emotion to it at all. Burnhams parents have barely featured before so the whole relationship had to be sold in this one episode, which isn't by any means impossible - TOS used to do that - but isn't done here. When they have exactly two conversations and in the first one Burnmom is standoffish, dismissive, and tells Burnham she's given up on hope, there's nothing to pay off later in conversation two where suddenly she pulls a complete 180. In the midst of a firefight we are supposed to be appreciating this "don't grieve admiral" type scene that is the payoff to a relationship we haven't seen. The actors tried, but it's completely cold. It would actually have been more impactive, I think, if Burnmom had kept to her original attitude and instead we'd watched Burnham having to come to terms with the fact that the mom she knew died a millennium hence from a thousand traumatic failures, and was replaced with this broken shell. Instead they decided to try for both in the space of forty-five minutes, and ended up landing neither.