Using acetone instead of acetonitrile on reverse-phase prep-HPLC
If you want to go completely green, you should use ethanol. 
In many sectors it is considered the only green solvent (except for water of course). 
Then, to be really green, you should make sure that it comes from fermentation, not from synthesis. 
This quality exists. 

The only problem with ethanol is the same as with acetonitrile, the price. 
In this case it is due to the taxes that it normally has. 
However, if you are working for some institution, it is probable that you can buy it tax free. 

Another alternative is to use methanol. 
It is not so green, but you can call it wood alcohol.
Methanol works very well in HPLC. 
The only difference with acetonitrile is that the pressure in the system will be higher. 
This is normally not a problem because the equipment is designed for it. 

I prefer not to use acetone because it can give reaction with some compounds, or with itself to form isophorone or other condensation products. 
As Waylander correctly points out in his comment, the UV cut off of acetone is also a problem in case you are using UV detection. 

                 UV cut off (nm)
 acetonitrile        190
 methanol            205
 ethanol             210
 acetone             330


To change from one solvent to another you will have to change the gradient.