How do denominations that ordain women at the same time justify not ordaining homosexuals?

The Free Methodist Church has a long history of ordaining women; in fact women were pastoring Free Methodist churches before they had the right to vote in the United States. The head pastor of my own congregation from 1915-1916 was one Rev. Laura Lamb.

In 1891 B.T. Roberts, one of the denomination's founders, wrote an exhaustive analysis in which he discussed the verse you cite along with many others which are relevant to the question of whether women may, or may not, be ordained. His conclusion is that taking the scripture as a whole -- and not a verse or two out of context -- there is no prohibition whatsoever that forbids women to be ordained. The closing paragraphs read,

IN the preceding pages the following propositions have been clearly proved.

1. Man and woman were created equal, each possessing the same rights and privileges as the other.
2. At the fall, woman, because she was first in the transgression, was, as a punishment, made subject to her husband.
3. Christ re-enacted the primitive law and restored the original relation of equality of the sexes.
4. The objections to the equality of man and woman in the Christian Church, based upon the Bible, rest upon a wrong translation of some passages and a misinterpretation of others. The objections drawn from woman’s nature are fully overthrown by undisputed facts.
5. In the New Testament church, woman, as well as man, filled the office of Apostle, Prophet, Deacon or preacher, and Pastor. There is not the slightest evidence that the functions of any of these offices, when filled by a woman, were different from what they were when filled by a man.
6. Woman took a part in governing the Apostolic church. We come, then, to this final CONCLUSION: THE GOSPEL OF JESUS CHRIST, IN THE PROVISIONS WHICH IT MAKES, AND IN THE AGENCIES WHICH IT EMPLOYS, FOR THE SALVATION OF MANKIND, KNOWS NO DISTINCTION OF RACE, CONDITION, OR SEX, THEREFORE NO PERSON EVIDENTLY CALLED OF GOD TO THE GOSPEL MINISTRY, AND DULY QUALIFIED FOR IT, SHOULD BE REFUSED ORDINATION ON ACCOUNT OF RACE, CONDITION, OR SEX.

If you Google the title "Ordaining Women" you'll find both a free PDF of the book, as well as a reasonably-priced paperback.

That said, the FMC remains firmly biblical in its understanding of sexual sin. A contemporary discussion on the issues surrounding h*m*sexuality reads in part,

We will give clear biblical teaching on human sexuality and God’s intended role for sex in the human experience. In this area, h*m*sexual behavior cannot be seen as part of God’s intended role for human sexual expression, regardless of a person’s attraction. Pastors must be thoroughly informed and equipped to teach on sexuality and should seek guidance for materials and instruction from their superintendent and denominational leaders that assist them in teaching Biblical wisdom on these matters.

There's really nothing comparable between the two issues: no one thinks that being a woman is sinful, but many Christian denominations think that all sex outside of heterosexual marriage is sinful.

When we look the passages which give the criteria for church leaders such as 1 Timothy 3 we see several distinct criteria:

1. being above reproach
2. a husband of one wife
3. self controlled and not a drunk
4. hospitable
5. able to teach
6. not violent or greedy
7. takes care of his own house
8. not a recent convert
9. well regarded in the community

Some of these are inherently vague - an elder is not to be a recent convert, but Paul doesn't specify what "recent" means. Some people might think that five years is still too young a Christian, others think that only one or two is acceptable. Others would take the principle more generally, and say that the time a person has been a Christian doesn't matter, but how spiritually mature they are does.

Similarly, the requirement that they're the husband of one wife is contentious. Does it just prohibit polygamous husbands? What about divorced husbands? What about single men?

It's clear that Paul assumes the elders will be men. But is that an assumption we can do away with, or is that an essential part of the role description? Christians disagree greatly over that question. Some churches will not appoint women to be elders/ministers/priests, others will. Both sides have good arguments.

But what is indisputable is that the candidate's moral character cannot be ignored. I only listed some of the prohibitions in 1 Timothy 3, Paul gives more! No one who is in unrepentant sin is qualified to lead a church. If a church thinks that h*m*sexual sex is sinful then they can refuse to ordain people in h*m*sexual relationships while ordaining women without being inconsistent in the slightest.