Thank you for reaching out to us. We appreciate the sensitive nature of this question and the special challenges that niddah observance presents to a couple during wartime.
It is halachically permissible to use hormonal means to manipulate the cycle, and in wartime this includes going on contraceptives. Sometimes, when a woman has advance notice of when her husband likely will or will not return home, she can use progesterone short-term to push off or move up the cycle a bit. In many cases, using a standard contraceptive pill is appealing, because it allows for this type of manipulation and also for the possibility of extending the cycle in general by taking more active pills in a row, leaving less frequent breaks between them, so that niddah questions arise substantially less often.
Your physician is the best address for discussing possible courses of action or a specific regimen for you. Be sure to mention that you would like to minimize staining and breakthrough bleeding as much as possible. We recommend taking a look at our page on manipulating cycles and our discussion of staying tehorah in wartime, which raise important points to consider.
Please be in touch with any further questions. May we hear besorot tovot!