The president signed the FY09 Defense Bills into law so DoD has Total Obligational Authority (TOA), but that does not mean they won't hold back on executing as planned. OSD puts a percentage of funding or certain items on withhold all the time and so does Dept of the Navy. Priorities and direction change all the time. What began as the President's Budget submit of FY09 was submitted to Congress in Feb 08 and sent to OSD from Navy in summer of 07. That's the last chance Navy had any options to manipulate it. Likewise, POM 10 budget data from the Navy is already at OSD and all hands are getting ready to have to rewicker that as well as PR 11 once direction is received. In a "normal" year (if there is such a thing), adjustments are made via an Omnibus reprogramming request mid Fiscal year to adjust for changes in service/OSD desires. In other words, OSD and the services can spend appropriated dollars for anything other than what they were signed into law for, but they can "not spend" appropriated dollars and either ask for reprogramming action from Congress (so they can spend it something else) or a rescission of funding (these are requests to not spend funds at all, usually when earmarks or "pork" items are included in a Defense Bill that the service does not want to execute; Congress can agree or direct funds be spent anyway).
So, yes, services or OSD can direct them to not spend according to the "budget". The next six months at very least will not be fun times to be in jobs associated with programming or budgeting (as if they are ever fun).