"Don't do anything that you wouldn't be prepared to talk about on the 6 o'clock news." (Mike Hutcheson)
Do you hold strong viewpoints or beliefs (ethical, political, ideological, religious, moral, etc.) that you would seek to preserve at the risk of losing work, or a client (as an agency owner), or even losing your job (as an employee)? Or would you compromise your convictions to keep the peace, keep your job, or make money?
For example, what would happen if you were vehemently opposed to vivisection and you were asked to work on a campaign for a cosmetics company you knew was actively involved in animal testing? What if you were a Jewish account manager who was asked to take on a bacon company as a client?
Agency owners and managers will have their own set of criteria by which they choose the set of clients that they will work with. Some agencies will turn down work they deem socially unacceptable, or reprehensible, but - as an employee - you can't guarantee that their decisions will align with your values.
Before taking any agency account management position it pays to look at the agency's client list and see if their clients resonate well with you. You should know exactly which account(s) you will be personally responsible for in your new role, as once you have signed your employment contract, taking a stand can be more difficult.
If you find your values are being compromised, you'll need to talk with your manager about the situation and let her know you'd prefer not to work on a particular project or with a particular client. It's important to explain why, and how strongly you feel. It's also important that you enter into this type of conversation with a solution as to how your manager can deal with the problem you are now presenting. She is going to have to resource the account (or project) with someone else, so you need to have thought this through before saying anything - otherwise you may be given an ultimatum to do the work "or else".
Not all managers are going to be sympathetic to your values, and not all situations are going to be easy to resolve. If you are going to take a strong stand, then you also need to be prepared to lose your job. Only you can decide if you have a line that you won't cross and how important staying true to that line is to you.