No, a subvariety of a principally polarized abelian variety need not be principally polarizable. This follows from:
1) Not every abelian variety is principally polarizable. (E.g. there are abelian varieties which are not isomorphic to their dual abelian variety.)
2) By the Zarhin trick, for any abelian variety $A$, $(A \times A^{\vee})^4$ is principally polarizable.
With regard to your argument: it is not true that any subvariety of an abelian variety is necessarily a direct factor. This is only true up to isogeny (and, indeed, every abelian variety over an algebraically closed field is isogenous to a principally polarized abelian variety).