I recall in the episode, "Take Two Aspirin, and Half a Pint of Porpoise Milk", Darrin visits a witch pharmacy to get certain items for a potion Aunt Clara was working on to try and cure Samantha of her square green spots disease; while the pharmacist tends to Darrin, he remarks, "You know you're the first customer I've seen in days? Nowadays, everybody uses them instant spells, just one quick incantation, and it's all over." which begs that question, if a witch disease can be cured with instant spells and incanations, then why don't they ever do that? And also, what need would they have for witch doctors such as the aforementioned witch pharmacist, and even Dr. Bombay?
There may not have been a spell to deal with that particular disease (which may not come up often enough to require one).
The more I think about it, the more of a jerk Endora comes off as. Witches are tremendously long-lived, living centuries or millenia (Maurice remembers the Roman Empire, and he's only in late middle age - at most), and however true Samantha's love for Darren, he'll only be around for a few decades. In terms of witches' lifespans, that's pretty well nothing, so couldn't she put up with him for her daughter's sake?
The earlier episodes emphasize that Endora is mainly concerned for Samantha's well-being and that of her grandchildren (who are, after all, half-mortal). In fact, Endora even goes as far as to tell Darrin it's not personal and sometimes even helps Darrin—and let's face it, Darrin isn't entirely innocent either. Flanderization of both characters over the course of the series made both of them more unpleasant (to the consternation of all of the actors involved).
This doesn't directly answer your question, but I recall reading a rather well-written fanfic, that took place shortly after Tabitha's birth, in which Samantha receives the news that Darrin was involved in a terrible car accident, and that he wasn't expected to live. Samantha was devastated, but took off for some place that almost seemed similar to The Adjustment Bureau, in which people's lives were "stored" onto external discs and such; Samantha spoke with whoever was in charge, explained the situation, and asked if the contents on Darrin's disc could be altered, so he could have a chance to see his daughter grow up, among other things. The supervisor agreed, and did just that; sure enough, Darrin, "Miraculously" recovers from the accident, however, he was aware of what happened, and even though he always wanted Sam to not use witchcraft, for this one time, he was grateful that she did, so he could be there for both her and Tabitha. Again, that was just a fanfic, but I imagine that, perhaps, somehow, Samantha would be able to find a way to prolong Darrin's life. Either that, or maybe, being a supernatural being, she and Darrin could still remain together in spirit.
The lifespan issue may be the major problem. Endora and the rest of Samantha's family, could have legitimate concerns that her Half-Human Hybrid children with Darrin will not enjoy the Wizards Live Longer trait. Sure, Endora is probably just fine with the idea of Darrin dying of old age in six or seven decades. But what about her grandchildren? Also, Samantha is being perhaps a bit overly-idealistic, since she would have very little experience with human aging. Endora may not think Samantha is really ready to cope with a husband who will face illness and infirmity, followed by death.