 There are a number of options here for the would-be methodological naturalist. You might simply say that such miracles occurred, that they did involve violations of law, but that they are outside your science. They are simply exceptions to the rule. End of argument. A little abrupt, but not flatly inconsistent with calling yourself a theist. You say normally God works through law but, for our salvation, miracles outside law were necessary. Or you might say that miracles occur but that they are compatible with science, or at least not incompatible. Jesus was in a trance and the cure for cancer after the prayers to Saint Bernadette was according to rare, unknown, but genuine laws. This position is less abrupt, although you might worry whether this strategy is truly Christian, in letter or in spirit. It seems a little bit of a cheat to say that the Jesus taken down from the cross was truly not dead, and the marriage at Cana starts to sound like outright fraud. Of course, you can start stripping away at more and more miracles, downgrading them to regular occurrences blown up and magnified by the Apostles, but in the end this rather defeats the whole purpose.