Update: the following code proposed by Lukas works perfectly. I have tested both fraction or $a/b$ form, both work. I have revised the code a little bit, to make it more flexible:
MakeBoxes[Sin[Rational[1, 2] Subscript[\[Alpha]_, i_]],
StandardForm] :=
MakeBoxes[Subscript["s", Subscript[Overscript[\[Alpha], _], i]],
StandardForm]
MakeBoxes[Cos[Rational[1, 2] Subscript[\[Alpha]_, i_]],
StandardForm] :=
MakeBoxes[Subscript["c", Subscript[Overscript[\[Alpha], _], i]],
StandardForm]
I learnt that we can use Makeboxes to display Sin[\alpha_i] as $s_{\alpha_i}$ as follows:
(*MakeBoxes[Sin[Subscript[\[Alpha],i_]],StandardForm]:=
MakeBoxes[Subscript[Subscript["s",\[Alpha]],i],StandardForm]
but can't find a way to make Sin[Subscript[[Alpha],i]/2] display as $s_{\bar{\alpha}_i}$, regardless of in fraction form or in $a/b$ form. I have been looking for this for quite a long time, but with no luck. I checked the documentation, but can't understand how Makeboxes works, especially in this context.
Could someone help to produce such a way so that it can take effect on both calculations involving fraction form or $a/b$ form? It'd be even better if some explanation on how to do it is provided.