You can override the current !important value by another one like
.col{ color:red !important; }
.col{ color:green; } // wont work
.col{ color:blue !important; } // will work and set color blue instead of red
DEMO.
Update :
This question is not about JavaScript but as an alternative you can accomplish the task using these technique, remove the rule using JavaScript and then add a new rule again.
function getCSSRule(ruleName, deleteFlag) {               
   ruleName=ruleName.toLowerCase();                       
   if (document.styleSheets) {                            
      for (var i=0; i<document.styleSheets.length; i++) { 
          var styleSheet=document.styleSheets[i];          
         var ii=0;                                        
         var cssRule=false;                               
         do {                                             
            if (styleSheet.cssRules) {                    
                cssRule = styleSheet.cssRules[ii];         
            } else {                                      
                cssRule = styleSheet.rules[ii];            
            }                                             
            if (cssRule)  {                               
                if (cssRule.selectorText.toLowerCase()==ruleName) { 
                    if (deleteFlag=='delete') {             
                        if (styleSheet.cssRules) {           
                            styleSheet.deleteRule(ii);        
                        } else {                             
                            styleSheet.removeRule(ii);        
                        }                                    
                        return true;                         
                    } else {                                
                    return cssRule;                      
                }                                       
            }                                          
        }                                             
        ii++;                                         
        } while (cssRule)                                
      }                                                   
   }                                                      
   return false;                                          
}                                                         
function killCSSRule(ruleName) {                          
    return getCSSRule(ruleName,'delete');                  
}                                                         
function addCSSRule(ruleName, v) {                        
    if (document.styleSheets) {                            
        if (!getCSSRule(ruleName)) {                        
            if (document.styleSheets[0].addRule) {           
                document.styleSheets[0].addRule(ruleName, v,0);
            } else {                                         
                document.styleSheets[0].insertRule(ruleName+'{'+v+'}', 0);
            }                                                
        }                                                   
    }                                                      
   return getCSSRule(ruleName);
}
// Check the rule before deleting
console.log(getCSSRule('.col')); // .col { color:red !important; }
// At first remove the current rule
killCSSRule('.col');
// Now assign nre rule
addCSSRule('.col', 'color: red');
// Check the rule after deleting
console.log(getCSSRule('.col')); // .col { color:red; }
DEMO. ( Source : Totally Pwn CSS with Javascript )