Belgarion and Ce'Nedra were prophesied to marry - she had to be the "Queen of the World". This simply had to happen, whether the marriage would be doomed to eventual failure or not (unlike Polgara).
However, it's not so clear that the two are as unevenly matched as Polgara and her husband, who was only a normal human. In particular, Ce'Nedra is a Dryad, although she doesn't have the ability to use the Will and the Word, she is a monster (in the Ulgo sense), at least partially.
This means that the equity in lifespan between husband and wife isn't as great (a Dryad lives as long as her tree does). Belgarion could probably still live longer, but Ce'Nedra could certainly live for thousands of years.
Although Ce'Nedra doesn't have the magical abilities that her husband does, she does have other attributes (e.g. from being a Dryad, and from the amulet) that make their marriage more equal than if Belgarion had married a regular human.
In addition, Polgara's sacrifice isn't actually a sacrifice (since rather than losing her power Durnik is granted equal power), it is a test: she doesn't actually give anything up, she merely has to prove that she would be willing to. This doesn't negate Belgarath's comment, but it does intimate that if Belgarion and Ce'Nedra were not sufficiently matched the gods would do something about that.