I do not know all the details of your husband's deployment or living arrangements.
However, generally, military members get to disregard up to 10 years of he qualifying period for the capital gains exclusion. Read this: http://www.irs.gov/pub/irs-news/ir-03-132.pdf
This disregarded period, however, is not explicitly applied to a situation where you sold a part of your property.
Having spent 28 years in the military, during my prior career, I can tell you that the "Family Readiness Group" is not supposed to give direct tax advise, and they may have lead you astray. Family Readiness should have been advising to not do any big decisions "alone" while he was away. The issue is related to family integration and re-integration after a long period of separation. I ran a Family Readiness Group for over a year, and help at the one in Ft. Dix. We focus on not doing major decisions without the husband, while he is away. That did not preclude the two of them making plans and letting the wife implement them accordingly in his absence.
What this means is that you may have received bad advise from the Family Readiness.
Lets put that aside however, for now.
What you will need in this circumstance is one of two approaches.
1. File the return as if the sale occurred implementing the rule for disregarding the qualifying period for the capital gains exclusion, and apply it to the two year rule for selling your house. that is disregarding the period of his deployment, and treat it as if the sell was on time. If the IRS disagrees with this, they will contact you, and you can then offer an explanation regarding the rules for disregarding. If they accept your explanation, then you are ok. If they do not, then you can still appeal to the tax court. The IRS will provide appeal instructions. Your husband's JAG should be able to provide legal support for filing such appeals. The JAG is the IRS VITA for military services.
2. You can apply for a private letter ruling to the IRS to determine before filing or after filing, if the rules to allow soldiers to suspend the waiting period, also applies to the rule to sell the home and include the attached land sold separately. Again, the JAG should be able to help you with writing up the private letter ruling. http://www.irs.gov/faqs/faq/0,,id=199552,00.html