There's a simple solution to afford a greater weight to the loss while still keeping the rebirth cycle: have the Digimon be completely new when they're reborn. No memories, no traces of who they originally were. How then, would this affect the children who lose their partners in the series?
In Takeru's case, it'd provide him with a more solid foundation for his fear of losing Patamon again, and hatred of evil and destruction in 02, particularly for those unsatisfied with his character's "sudden" turnaround. However, I think it'd also provide Takeru with more of a character arc in Adventure--he not only would have to face the grief that, no, the Patamon he knew is not coming back, as well as fight back the resentment of the fact that this new Patamon in front of him is a "replacement," but also have to bear the responsibility of raising and looking after the little fella.
Takeru's care of Patamon, in turn, earns some resentment from Patamon himself, irked that his partner is so overprotective of him when he knows he's the one meant to protect him, and with the knowledge that he has an extremely powerful evolutionary state at that. This is what eventually leads Takeru to a moment of understanding both Patamon's position of being underestimated and babied, as well as why his brother is so overbearing and underestimating of him. It'd provide a bit of closure for both the brothers' arcs in this season.
As for Ken...
I've debated whether having Wormmon be given the same proposed fate as Patamon would be needlessly cruel to Ken, after he spent an entire existential episode coming to terms with himself (one that continues as the series progresses). I've concluded that it might be, but it also might bring about some potentially interesting developments.
Ken would have to tell the new Wormmon about how his life was lost, how he, Ken, was at fault for it, his past as the Digimon Kaiser, and his current journey to atone for it. Having Ken interact with an innocent, blank slate that knows nothing but to love and protect his partner, could be meaningful to Ken's development. Ken would have to lay out all the harsh realities of what he's done in the past, acknowledging he could still be capable of committing them again, while the new Wormmon puzzles over how gentle, kind Ken in front of him was or could be a cruel person. It'd be frustrating and endearing for the both of them, a practice in attempting to reach a sense of balance--Ken trying to get Wormmon to understand what he's done, while Wormmon tries to remind him of the genuine goodness inside of him; eventually learning how these attributes can coexist.
More interestingly, however, is that Ken would have to realize he couldn't possibly impose the same expectations of the old Wormmon on to the new Wormmon--something that doesn't come to him as immediately as "Warn Wormmon that I was once capable of these awful things." Like Takeru, he'd struggle with having an entirely new partner; unlike Takeru, his realization throughout raising his partner isn't based upon having had an overbearing brother, but that his parents placed the same high expectations on him as a "replacement" when his brother died. While he, too, understands where his parents were coming from, Ken also understands that he can't possibly have the new Wormmon undergo the same ordeal he did, and has to learn to love him as his own individual, just as his parents learn to do so with him.
This gentle, gradual understanding, will ultimately be what leads Wormmon (to Ken's surprise, having never intended this to happen) to have the ability to evolve to Stingmon. (When and where, I can't be sure, but I think it'd serve as a nice wrap-up point to this proposed "Ken forges a bond with the new Wormmon" mini-arc.)