Flags having a stronger influence than upvoting is a necessary algorithmic check against genuinely bad behavior/brigading, not disagreement. In general it works as intended, which is the best you can do without something potentially worse.
Are there any stats available on the weighting ratios such as flags to upvotes, likes and comments per post after flagging, average time to frontpage to flag?
(G summarises the following[0], but a definitive source would clear up what the necessary algorithmic checks are).