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Robert -- this could be fixed so it works exactly like you want, but it requires writing some code in Cython, and pretty advanced knowledge of Sage internals. One potential workaround is to simply multiply over ZZ, then reduce the answer, e.g., do something like this:

sage: M = random_matrix(ZZ,100)
sage: v = random_matrix(ZZ,100,1)
sage: timeit('(M*v) % 11^3')
625 loops, best of 3: 631 µs per loop

which beats all the following by a lot:

sage: M = random_matrix(ZZ,100)
sage: v = random_vector(Integers(11^3),100)
sage: timeit('M*v')
125 loops, best of 3: 2.55 ms per loop

sage: M = random_matrix(ZZ,100)
sage: v = random_matrix(Integers(11^3),100,1)
sage: timeit('M*v')
125 loops, best of 3: 4.83 ms per loop

sage: M = random_matrix(ZZ,100)
sage: v = random_vector(ZZ,100)
sage: timeit('(M*v) % 11^3')
125 loops, best of 3: 4.42 ms per loop

Incidentally, "write code to compute with overconvergent modular symbols" is something Ben Lundell and I at UW have been wanting to do in the near future to. Maybe we can coordinate? Email us.