To be fair, if anything comes between an atheist and a theist it probably won't be theism itself. Instead, one of the things most likely to cause problems will be religion - not every theist is religious, and not every religious person is a theist. What this means is that specific doctrines and dogmas are most likely to cause problems and will have to be watched closely.
As discussed previously, in order for a marriage between a theist and an atheist to work it is necessary for both to be able to not only tolerate one anothers position, but to respect them as people as well. An absence of respect for the person you are married to will kill a marriage quickly. Because of this, the doctrines which are most likely to interfere with a marriage are those which encourage or cause the religious believer to lose respect for their spouse.
For example, there are many religious people who believe that a marriage must be based on God and/or that a married couple must always put God first but a marriage between an atheist and a theist obviously won't be able to do that. Another example would be the common Christian belief that only Christians will go to heaven and that atheists certainly will not, an obvious problem if such a Christian is married to an atheist.
There is a very good chance for conflict in a marriage if such doctrines come into play. It isn't unreasonable to argue that when a person makes their religion a significant basis for a marriage and their (prospective) partner doesn't share that religion (for whatever reason), then the marriage is in trouble from the beginning.
If you are concerned that your differences with someone might prevent a possible marriage, it would be a serious error to focus solely on the fact that one of you is a theist and the other not, or even that one of you is religious and the other not. Instead, it is necessary to take a closer look at the specific doctrines and dogmas which the religious person holds and consider how they might affect that person's perspective on non-adherents and a marriage with a non-adherent.