I think you're wrong. The Queen will not attend the civil ceremony, but will attend the Blessing at the chapel. Looks to me like she is going to the religious portion specifically. Maybe there's some Royal protocol since she's the Head of the Church.
The excuse the Palace is putting out for the Queen not attending is fairly insubstantial - they're suggesting her attendance would automatically make a "simple ceremony", not simple at all.
Not really. Security, et al - all those complex arrangements were taking place anyway. This indicates her displeasure with either the wedding itself, or how it's been done, which admittedly, has been full of cock ups.
Regards, Ivan