Personally, I do not think you would be a coward if you go underground because ultimately your practise is between Dorje Shugden and yourself, your guru and yourself and not between you and what you are in the eyes of others. I have no doubt that many are in the situation where they are caught between a pro-shugden and anti-shugden teacher or monastery and face tremendous dilemma in their decision making. It's like choosing your left hand or your right hand - either way, it's tough.
Therefore, going underground does not make you a coward. If it protects your guru, protects you, protects those around you and yet you are still able to benefit others in your faith, then it totally beats those going around and shunning Shugden practitioners.
Afterall, what is a corward? A real coward is "a person who lacks courage in facing danger, difficulty, opposition, pain, etc.; a timid or easily intimidated person." In other words, a coward does not take responsibility for and of others for fear of the difficulties they have to endure. That's a coward. So if your motivation to go underground doesn't fall according to those lines, then you are not a coward.