It does break a relationship because if you are flirting with someone and then this potential romance wants to have sex with you (for the first time) but you reject him/her...you can expect said person to believe you don't find him/her attractive and consequently leave you.
Let me see if I understand this example; Someone is basically pressuring someone else into having sex on the threat of ending the relationship based on personal insecurities if the other person do not agree to have sex even though the other someone does not want to for different reasons that are not necessarily tied to religion.
One reason that applies to Mass Effect 2 could be incredible poor timing given that they are about to embark on a suicide mission and Shepard is possibly under a great deal of stress as well as potentially dealing with guilt over what happened to the crew meaning that they understandably may not to be in the mood and may be more interested in emotional support that is not tied to the sexual variety.
Additionally, I believe there is also a duty-first reason since with some of the romances, there are factors that could result in some of the crew or Shepard themselves becoming incapacitated if they engage in a sexual act meaning it may compromised the combat and mental performance of Shepard or the crew thereby lowering the chances of the mission's success.