I was under the impression riya and ali were always to be a thing even if the triangle does happen. there have been ample signs- the ali riya card picked at riya's birthday, nanno showing riya's pic to ali by mistake as a potential marriage prospect to him, there are loads of sign that though he loves avni, it'll be riya in his life. i personally think that the ali and riya story is very important. avni's story is her revenge and how she gets over that revenge, but this serial had a lot more important issues- the struggle of interfaith relationships and legitimacy of love. aliya relationship would help bring that back up as well. it would be interesting to see that dimension of the story come full circle as well.
I think it would be a script change if they did something to change that storyline- like make ali or riya negative to fill in for dayavanti as she loses mental balance as per the latest segments. i do think ali is upset but right now, he thinks avni will just leave neil and this marriage will be annulled. we will know his real reaction when avni and neil do try to make their marriage work. or maybe riya and him will find the comfort and love they both deserve after the heart breaks and the toxic environment they grew up with.