This is rubbish- the action of the mapping class group on homology is by $Sp_2g(\mathbbZ))$, which for $g>1$ is a proper subgroup of $GL_2g(\mathbbZ)$, the group of base-changes of $H_1(F)$.
As an example of what you can't do with a diffeomorphism of a surface, consider a disc with 4 bands A,B,C,D attached, so the order of the end sements is $A^+B^-A^-B^+C^+D^-C^-D^+$, together forming a surface. A basis a,b,c,d for $H_1(F)$ is given by this picture as 4 loops going through the cores of the bands A,B,C,D correspondingly. You can add a to b, b to c, c to d, or d to a by diffeomorphism of F (sliding adjacent bands over one another). However, although you can add a to c algebraically, because bands A and C are "not adjacent in F", there is no corresponding diffeomorphism of $F$.
One place this mistake manifests itself (cranking up the level of terminology for a second) is in thinking that unimodular congruence of a Seifert matrix corresponds to ambient isotopy of a Seifert surface.
A related common mistake (closely related to this question):
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