Firstly: 

We praise Allaah for having blessed your wife with guidance and choosing her to be one of the Muslims. This is a great and precious blessing which should be protected and nurtured. Try to support her in learning the rulings of Islam, strengthening her faith by doing acts of obedience and keeping away from sin. We ask Allaah to enable you to do all that is good. 

Secondly: 

We do not think that she has any excuse for uncovering her head or for wearing pants, unless she is afraid that her family will harm her if they find out about her being Muslim. Allaah says (interpretation of the meaning):

“Verily, as for those whom the angels take (in death) while they are wronging themselves (as they stayed among the disbelievers even though emigration was obligatory for them), they (angels) say (to them): ‘In what (condition) were you?’ They reply: ‘We were weak and oppressed on the earth.’ They (angels) say: ‘Was not the earth of Allaah spacious enough for you to emigrate therein?’ Such men will find their abode in Hell — what an evil destination!

98. Except the weak ones among men, women and children who cannot devise a plan, nor are they able to direct their way”

[al-Nisa’ 4:97, 98]

Your wife -- as it appears to us from what you say -- is not one of those who are weak and oppressed, because she is not living with her family and she has nothing to fear from them; rather the most that can be said is that she is afraid of her ties with them being severed. 

Al-Aloosi (may Allaah have mercy on him) said: 

What is meant is that they tried to justify their shortcomings in showing their Islam openly and falling short in carrying out their religious duties on the grounds that they were weak and oppressed, which was why they could not carry out their religious duties among the people of Makkah; therefore they did not do much. Or they made excuses for not going out with them [the Muslims, to Madeenah] and becoming a part of their [Muslim] community on the grounds that they were helpless and under the control of the non-Muslims of Makkah. Whatever the case, the angels did not accept this from them. 

Tafseer al-Aloosi, 4/196 

And he (may Allaah have mercy on him) said: 

Every believer who finds himself in a place where he cannot show his religion openly because of the opposition of those who are not Muslims is obliged to migrate to a place where he can show his religion openly. It is not permissible for him at all to stay there and conceal his religion and to make the excuse that he is weak and oppressed, because Allaah's earth is vast and spacious. 

Yes, if he is one of those who have a shar’i excuse for not migrating, such as children, women, the blind, those who are detained, those whom the non-Muslims scare with threats to kill them or to kill their children or fathers or mothers, in cases where he thinks that what they are scaring him with is most likely to happen -- whether that killing is by beheading, withholding food and so on -- then in that case it is permissible for him to stay with the non-Muslims and to go along with them as much it is necessary, but he must strive to find ways to escape and flee for the sake of his religion. End quote. 

Tafseer al-Aloosi, 2/479 

What we advise you to do -- if your wife is not afraid that she may be harmed by her family -- is to tell them that she has become Muslim and to send someone to them to inform them about that, and to continue to uphold ties with them and treat them kindly. 

Perhaps one of the greatest benefits of her showing her Islam openly is that she will become keen to call her family to Islam and she will start to look for suitable ways to do that, such as corresponding with them, talking to them, and sending them audiovisual materials on Islam. Perhaps Allaah will guide them to enter Islam, and that will be included in the balance of your good deeds. Thus your wife will be safe from committing those haraam actions, she will have established proof against her family, she will have discharged her responsibilities before Allaah and she will have striven to guide them and save them, because it is not right for her to have the blessing of Islam and deprive her family of it. 

We ask Allaah to help and guide you. 

And Allaah knows best.