It says on the archetypes that you can choose if you wish to replace a class feature. However, there are some you must take regardless.
I find the only worth while Alternative class feature for the cleric was the Evangelist. Trading A domain, armor and shield proficiency and the occasional Channel energy for bardic songs and to yell louder.
However, trading Spontaneous healing spells? That is optional right? Although the very flavorful spontaneous mind controlling spells can be used quite nicely. Healing and curing is something I just would never want to lose as a cleric.
It is my understanding that with archetypes, it is all or nothing. If you decide to pick and choose abilities from an archetype, then that will end up being a houserule that you'll need your GM's permission for.
Archtypes are all or nothing.
You either select an archtype and replace all the abilities with the new ones, or you don't select and archtype and you keep the base class abilities.
You do Not get to pick which ones you keep and which ones you replace.
Its all or nothing.
-S
An evangelist isn't a healer. They will convert you, but leave the healing to the stick of magical positive energy pewpewing.