The real issue here is making sure DUNGEONMASTERS are aware of what these SoD effects and the monsters that use them mean to their adventures and encounter design.
In 4E, one of the bigger issues was that it was only the monster's power level (minion/standard/elite/solo) that told DMs the kind of thing they were throwing at their parties. Actual effects were not demarcated in that way. As a result, we'd hear stories of DMs creating encounters with 5+ monsters who dished out the Weakened effect, or the Dazed effect etc., because they didn't know any better. And this is the same problem that could creep up with the use of SoD effects. Without being very, very clear about what using like five basilisks in a fight could mean... you'll end up with lots of poorly thought-out encounters with a lot of unexpectedly unwanted results.
I myself have no problems with the regular old Save of Die spells... if for no other reason that I am acutely aware of what they CAN do. Thus, I don't introduce them into an adventure if I'm not willing to accept whatever results might come from them. I think DDN can certainly follow along these lines... it's just imperative that the writers of the Monster Manual make explicit the fact of just what these monsters with these abilities can do.
There are two ways I think you could do it. First is to just put all monsters with SoD effects in Appendix A of the DDN Monster Manual. Appendix A is the "deadliest of the deadly" monster section, and thus any DM who uses a creature from it should really think long and hard before selecting it.
Now if that option doesn't sit well with people (moving certain monsters out of the alphabetically listings into their own little pen)... the second is to make all these monsters with Death, Disintegrate, Petrification, Instant Killing Poison etc. all SOLO monsters (assuming the interpretation of 4E's monster power levels.) That was the one thing they really tried to hit home for us in 4E. The Solo was supposed to be able to take on a party of 5 pretty well (at least in theory). We knew that using a Solo monster was meant to be a big deal. Thus, in DDN if you only gave SoD effects to monsters who are meant to be "Solo"... it immediately tells the DM that this monsters isn't your prototypical one. It's a big deal. It's power is meant to be looked at a little more closely. It's not a creature you send three or four of them out there just on a whim.
If the beholder and the medusa and the ancient dragons have powers that are meant to kick the ever-living crap out of a party and potentially kill them on sight... just make sure the DM is aware of this going in so he makes the active choice to throw this encounter at his players.