Is it permissible to supplicate for a matter after a clear Istikhara has diverted it, and after ceasing active pursuit of it? And is that considered an objection to divine decree? And is it permissible to supplicate that Allah replace it with something better if it contains evil?

Your supplication for something to be facilitated after performing Istikhara, or for it to be averted from you, does not contradict contentment with divine decree. It might be that it is not good for you at that particular time, but it comes to you later due to your supplication. It is permissible for a servant to supplicate for the facilitation of what they desire and for Allah to make it good for them, as evidenced by the Prophet's (peace be upon him) supplication for Aisha: "O Allah, I ask You for all good, both immediate and delayed, that which I know and that which I do not know... And I ask You to make every decree You have decreed for me good." And as it was narrated: "When one of you wishes for something, let him ask for much, for he is only asking his Lord." Supplication can avert a decree and ward off affliction, and it is part of destiny. One should rely upon Allah and ponder over His saying: "But perhaps you hate a thing and it is good for you; and perhaps you love a thing and it is bad for you. And Allah knows, while you know not."