IRCop is different from ChanOp. In regards to the proper way IRC is to be run, IRCops are not to interfere with channel affairs. RFC1459 states that oper status is used to maintain the server, not channels. So traditionally, services packages will keep access separate because of that. As far as your "higher level of access" goes, it's not correct. IRCops don't have higher access, they have special access to keep the server running smoothly. IRCops are users too, just like everyone else. The extra commands that are granted have nothing to do with channel maintenance (/connect, /squit, /kill, /kline). Some IRCds like Unreal and Bahamut convolute the separation that is there by allowing some IRCops the ability to op themselves but assure you that those commands are not required for an IRCop to do their job.
Just because you can op yourself, doesn't mean it's your channel to takeover. The channel still belongs to whomever registered it. If the channel is unregistered as in your case, the channel belongs to whomever is a chanop, thus why services requires you to be a chanop to register. If the channel in not registered and no one is a chanop then it belongs to no one.
IMVHO, Anope should not change this behaviour.