Your concern can be separated into two issues:
1) How a Christian should conduct him/herself in an academic environment hostile to Biblical ethics; and
2) in your own words, "I know our focus and priority is the gospel; to what extent should we go in protecting our families from the aggressive homosexual agenda and should we actively oppose gay marriage on a civil level?"
The second lends itself to fairly clear answers, in my opinion, so I will deal with that first. When Christians live in a culture saturated in sin (in this case, violations of the 7th Commandment), they will find that those around them "think it strange that ye run not with them to the same excess of riot, speaking evil of you." (1 Pet. 4:4) We are obligated, nonetheless, to obey God rather than man. In thinking of how to live out God's Law, we do well to remember the teaching of our Larger Catechism #99 (p. 237), which is on the interpretation of the Law. It lays out eight principles; most pertinent to our discussion are principles 7 and 8.
7) That what is forbidden or commanded to ourselves, we are bound, according to our places, to endeavor that it may be avoided or performed by others, according to the duty of their places.
8) That in what is commanded to others, we are bound, according to our places and callings, to be helpful to them; and to take heed of partaking with others in what is forbidden them.
These principles are supported in numerous places in the Bible; I will simply cite 1 Tim. 5:22. "Lay hands suddenly on no man, neither be partaker of other men's sins: keep thyself pure."
Thus, to whatever extent our families may be subjected to an aggressive homosexual agenda, we must be on guard. This begins by teaching our children a Biblical view of sexuality, which of course would address not only forbidden sexual practices, but more importantly the role of sex within Christian marriage as a gift with which to serve one's spouse. As gay marriage would certainly be a sin, then we ought to oppose it; to endorse it for any reason or in any form would be to encourage others to do that which is forbidden by God.
With regard to your academic environment, the matter is more complicated. The basic rule, of course, is to offend only with the Gospel. I commend you for making an effort to listen respectfully to offensive points of view. The challenge is to how to engage those productively. My own experience as a university student at a state school taught me that a Christian who disagrees with his or her professor (or department)'s philosophy must work at least twice as hard as other students. That is, you must know and understand the course material thoroughly so that you can identify its strengths as well as its weaknesses. Then you must research and discover the best arguments, Scriptural and otherwise, for your own positions. You must treat those with whom you disagree with intellectual respect: this is a straightforward application of the Golden Rule.
My experience, and the experience of many students in the humanities, is that professors are glad to engage with thoughtful students who hold different opinions. Thus, one ought not to assume a hostile reaction or a lower grade merely because one expresses explicitly Christian positions. At the same time, that may be the consequence of bearing Christian witness in your environment. Whatever may come, I encourage you to seek counsel on any specific matters from your pastor and elders, and also to meditate regularly on 1 Pet. 3:8-22. I think you will find the Spirit inspired this passage for persons in circumstances just like your own so that in all things you might always rest securely in the Cross of our Savior Jesus Christ.
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