How to send Javascript map as a parameter from lightning component to Apex server controller?

Don't use Map, just use a normal Object. Here's a demonstration:

Apex:

public class LightningMap {
    @AuraEnabled public static void doMap(Map<String, Object> values) {
        System.debug(values);
    }
}

Lightning Controller:

({
    doInit: function(component, event, helper) {
        var action = component.get("c.doMap");
        action.setParams(
            {
                "values": {
                    "Hello": 5,
                    "World": 15
                }
            }
        );
        action.setCallback(this, function(result) {} );
        $A.enqueueAction(action);
    }
})

Demo App:

<aura:application controller="LightningMap">
    <aura:handler name="init" value="{!this}" action="{!c.doInit}" />
</aura:application>

Logged output:

13:16:24.0 (1462121)|USER_DEBUG|[3]|DEBUG|{Hello=5, World=15}

---

For a more directly applicable version, this is probably what you want:

var mapToSend = {}
for (var key of valueMap.keys()) {
    mapToSend[key] = valueMap.get(key);
}
action.setParams({
    "name": cmp.get("v.name"),
    "params": mapToSend
});

UPDATE

Ok, I was bugged by this one and made my own test app.

The result is: you CAN have a Map. You just need to make sure it's declared in the markup and has a default="{}" attribute specified (I initially specified some keys, but you don't even need those, just empty braces)

So, component markup:

<aura:component controller="Your_Controller">
    <aura:attribute name="theMap" type="Map" default="{}"/>
    <aura:handler name="init" value="{!this}" action="{!c.doInit}" />
</aura:component>

Controller code:

({
    doInit : function(component, event, helper) {
        var action = component.get("c.testMap");
        var theMap = component.get("v.theMap");
        //add some params
        theMap["key1"]="blah1";
        theMap["key2"]="blah2";
        action.setParams({
           "params": theMap
        });
        action.setCallback(this, function(result) {} );
        $A.enqueueAction(action);
    }
})

Server side controller:

@AuraEnabled
public static void testMap(Map<String, Object> params){
    System.debug(JSON.serialize(params));
}

So you CAN have a Map. You just need to declare it in the markup! Hooray!!