In TNG "The Emissary", K'Ehyler says that Klingon-Human hybrids are possible "with a fair amount of help". Given how hard it would be for interspecies hybrids to be born without some genetic manipulation, is there an IVF exception to the ban on genetic engineering in the Star Trek universe (including EU materials) for helping interspecies couples conceive?
There's not a ban on genetic engineering.
Genetic engineering is totally allowed and used from time to time. For example, in Genesis, a virus causes dormant DNA from animals to re-activate in the enterprise crew, causing them to de-evolve into other animals. They then fix this, and restore the crew to normal.
Or in the Fight, Chakotay's family has a gene that causes them to have hallucinations. In him, it's suppressed. Aliens are trying to communicate with them, and destroying the ship from the 18th dimension. The doctor re-activates his gene fully, and the aliens help them escape.
They are against genetic augmentation, because of the past problems it has brought. They are fine with necessary medical genetic engineering to fix problems.
Fertility issues are likely within that allowed genetic engineering.