In the book Quintessential Cleric, they propose alternate versions of domains - for example, the death domain has 3 variations, say 'lay to rest', 'dying and nature', and 'necromantic death magics' (I do not have the book on me, this is just an attempt to describe the 'flavor'). It still limits you to a single spell per spell level in a domain, but it does allow for a more interesting / accurate style to each domain. As an argument for domains not being intended to have more spells then 1 per level, in no splat book, either for core d20 or in FR splat, have they offered spells to add to a domains list. RR adds spells to the domain list, plumping up certain domains to extreme while leaving others barren. You could, as a HR, have a wider list of spells in domains - but have clerics choose their 'domain' list of a single spell per LV from the wider selection. Sort of like having several variants or subgroups of a church, each taking slightly different assortments from the domains. Perhaps you could, as per the sorcerer, allow them to swap out spells at certain levels...
Then again, this is getting overly complex. Just call it a feat to add 3 related spells to your domain selection, no more then 3 spells per domain spell level.