We have mostly welcomed "freedom of conscience" ... even when that may have lead a pastor/session to "refrain" from just behavior, though firm lines were drawn leading up to the Civil War on slavery, and in the early 1970s, with regard to the ordination of women. On both of these matters, it was believed that a "house divided" could not serve the LORD or bear a faithful witness to the world.
With regard to the ordination of LGBTQ persons, it was saddening to me to note the numerous charges filed against pastors/sessions who, for reasons of conscience and Scripture, "violated" the "no ordination" ban for LGBTQ persons - those opposed to LGBTQ ordination were not willing to grant merit to "conscience," though now, at least on the matter or ordination, now allowed for LGBTQ persons, we grant "conscience" allowances - since ordination to local office is a matter of the local church, it's highly unlikely that any charges would be brought for not electing and ordaining an openly gay person. It will be interesting to see what would happen if a congregation nominates and elects a gay person, contrary to the wishes of the pastor. Would the pastor relent, or would the pastor invite in a neighboring pastor to preside for the ordination?
Should marriage equality become the law of the church, no pastor would be compelled to officiate at a same-gender marriage (in spite of the fears raised up on this matter by those opposed).
As you rightly note, it is a justice issue, though the opposed see it as a "biblical/tradition/theological/faith" issue. Because of the seriousness of their resistance, there's no need for them to be compelled to ordain an LGBTQ person, and if marriage equality prevails, there will be no mandate to officiate at same-gender marriage ceremonies.
I think time will take care of this, though not entirely eliminate it. After all, we still have pastors who resist the ordination of women, would not allow the knowing ordination of a gay person, and we have still church that continue to practice an institutional segregation.
Those who cannot abide by such things have options, of course. Folks/churches can always leave. Many a pastor, lots of members, and some churches, left for the UCC to find freedom of faith and life. Others left for the PCA and EPC to find theological safety and congruence. And now, on the conservative side of things, ECO offers refuge for those opposed to the full inclusion of LGBTQ persons in the life of the church.
In the matters of local ordination, and in the matter of marriage equality (should that come to pass), "freedom of conscience" is operative, in spite of the fact that those who favor ordination and marriage equality see it as a matter of justice. And why? It's a matter of kindness, recognizing that the "purity" of the church is hard to define, but the "unity" of the church isn't.