I don't share your assessment that Niffenegger merely brought up the concept of paradoxes and then dropped them. Within the book's massive pagecount are plenty of situations that are all about the concept of paradoxes and changing history; Niffenegger doesn't drop the concept, she comes down heavily on the side of "It doesn't happen; it can't happen; history is fated and set and deterministic". That's why the book is a tragedy -- the question of what would've happened had Clare not met Henry and been free to develop a relationship with Gomez is unanswerable, because it *did* happen and is the *only* thing that happens. Gomez wishing Henry's relationship to Clare could be undone is one of many instances of someone in the book trying to change something only to find that things are set and can't be changed -- ranging from Clare being unable to alter the picture she drew of Henry on a lark to Henry being unable to prevent his mother's death or Ingrid's suicide, all the way up to Henry's death itself, something Henry actually witnesses but remains powerless to prevent.

To me that's a powerful message, and indeed tied directly to the "soulmate" message at the core of the book; to believe in Fate and Destiny when it comes to good and happy things like "soulmates" is to also believe in it when it comes to sad depressing things like the ex you dumped for your soulmate spiraling into despair and shooting herself years later. It's about clinging to faith that these fated, unchanging events will somehow work out even if all indications point to the contrary (see the conversations with Clare in the Meadow about God, the conversations with Henry's doctor about whether he's an Ubermensch, the hints that the time-travel mechanism, despite its apparent overriding of conscious free will, may be some kind of unconscious "free will" playing out and bringing people where they need to be, etc.)

Niffenegger did write the book as an embittered single, and has claimed she started the story identifying more with Ingrid than Clare, so she's actually aware that this whole "soulmate" business hurts the people it leaves behind as much as it's wonderful and fulfilling and beautiful for the soulmates themselves; I think a lot of the fanbase doesn't get this, given that I found Ingrid and Gomez both to be strongly sympathetic characters on my first read and a lot of fans hate them.