Why do the earth sciences use mega-annum instead of mega-year?
Both mega-annum(Ma) and mega-year(Myr) designate one million years.  The distinction is that Ma is used to designate the time before present or geohistoric dates and Myr to designate a duration or span of time.  So if you want to say a rock is dated to 10 million years before the present you would use 10 Ma, and if you want to say that a rock is 10 million years old you would use 10 Myr.

There has been debate among scientific disciplines to simply adopt Ma as the standard unit.  However, the distinction that geologists have been using to distinguish between dates and durations for decades can best be illustrated as such:


  No one objects to the storming of the Bastille on 14 July 1789 (a
  date) or to the construction of Stonehenge from 2600–1600 BC (an
  interval specified by two dates). In the case of the latter, we say
  that the job took 1000 years, not 1000 BC. The distinction between
  geohistorical dates and spans of geological time is conceptually
  analogous. There is no internal inconsistency, and the International
  System of Units (SI) rules don’t apply to dates in either case because
  points in time are not units, even if they are specified in years
  (Aubry et al., 2009). The year, moreover, is not a part of the SI. It
  cannot be a “derived unit of time,” the designation proposed by the
  task group, because under SI conventions “derived units are products
  of powers of base units” (BIPM, 2006). The base unit for time is the
  second. The task group is thus intent on fixing a problem that doesn’t
  exist and in a manner that is at odds with their stated goal of
  “adherence to SI rules.”


The above quote is from the Geological Time Conventions and Symbols manuscript from 2011.  More detailed discussion can be found at this source.  This Science Blogs article from 2009 has some interesting discussions regarding this issue.