One way around it is a complete reversal of the Prime Directive.
According to the big PD, the advanced society of the Federation is not supposed to interfere in the natural evolution/development of lesser tech species/societies.
By definition, Khan and co. come from an era is that technologically (and socio-politically) less developed than that of the 23rd century. Who's to say that someone in the Federation will look at taking Khan's blood to revive Kirk was not a violation of the Prime Directive in reverse? That an element of a lesser developed society has interfered in the natural flow of life for a member of an advanced society. If that be the case said person tries to make, and said case wins over the courts, then Khan's blood or other regenerative capabilities could be considered off-limits for the Federation era.
There. Death is back in play.
As for the transwarp beaming....well...again, someone in Federation legal and ethics may look at that device, and state some kind of legalese/ethical dilemma on the uses of such a device, again gaining the ear of the courts...especially considering that the recently uncovered Section 31 (in the form of Khan) made such a devious use of the device after causing tremendous tragedy. Transwarp beaming could also be made illegal, and Scott's transwarp beaming theory be confiscated from Section 31, destroyed, never to be recovered.
There. Now we have use for starships again.