If you don't believe that it is due, appeal. Given the date (the normal time limit for 2008-09 expires on 05-04-2013) HMRC have probably issued this assessment to protect their position and will be expecting an appeal. But HMRC usually deal with these situations via Reg 80 charges on employers, so they are probably assessing you too just to be on the safe side.
Whilst you may be confident that the scheme was a legitimate arrangement, HMRC are unlikely to share your view. Indeed, looking at their latest stance they seem pretty confident ... http://www.hmrc.gov.uk/news/ebt-news0812.htm
HMRC has been successful in litigating cases which have involved EBTs as part of the arrangement(s) entered into by a company/employer. The most significant of these cases is HMRC Commissioners v PA Holdings Ltd  EWCA Civ. 1414 where the Court of Appeal decision upheld HMRC's arguments that an arrangement intended to deliver a bonus through an EBT was subject to tax and NICs as earnings.
HMRC considers that the Court of Appeal judgment supports its view that arrangements to avoid PAYE and NICs through the use of EBT structures do not work. HMRC's view in relation to EBTs is published in Spotlight 5 (see the link below). For many EBTs, the allocation is the point at which the funds go into a sub-trust for the individual employee or their family but ultimately when the charging point for PAYE and NIC arises will depend on the facts of the individual case.