API endpoint PUT /v3/projects/:id/merge_requests/:merge_request_id executes more than 100 SQL queries

This controller executes more than 100 SQL queries, the maximum number of queries allowed as per MR https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/16466. The number of queries should be reduced to less than 100 and the corresponding whitelisted sections of code (Gitlab::QueryLimiting.whitelist { ... }) should be removed.