The problem here is not your SOQL - necessarily - but rather that you are trying to display more than 1000 records on your VF page. This is not allowed. You should research standardSetController and set up pagination on your page - that should fix this problem.

I thought about pagination, but I figured I would like to limit the results on the VF page anyways - As I said, I will never be putting a contact to a client that is outside their heirarchy structure.

Essentially, as my company continues to grow, I do not want my employees to have to scroll through 20 pages of pagination to select the proper accounts. I'd like to just display the relavent child accounts, and have it summarize the information at this point in our process.

Edit: this also assumes that none of our clients have more than 999 'locations/accounts' in our system. If a client had more than 999 accounts, I'd like to have pagination take over, because we've now distilled the displayed accounts to those relavent to the contact - it just so happens that this is a very large client of ours!

I believe even with pagination you will encounter the error. The issue is with a collection limit being referenced on a visualforce page. Pagination does not change the actual size of the collection. You would need to use the new offset soql feature to do it this way...however...

There is a way to display more than 1000 records at a time using a list of a list. As a warning this will affect performance when displaying more than 1000 records. So be wary about how many records you want to display.

Here is some sample code.

public objectListOfLists List<List<Account>> {get; set;}

public void createLocationsList(){
        List<Account> tempList = new List<Account>();
        objectListOfLists = new List<List<Account>>();
        //loop through the query you had
        for (Account a : accounts){
            tempList.add(a);
            if (tempList.size() == 1000){
                objectListOfLists.add(tempList);
                tempList = new List<Account>();
            }
        }
        if(!tempList.isEmpty()){
            objectListOfLists.add(tempList);
        }
}

 Then...you will need to use an apex repeat along with a pageblock table. The repeat will iterate over each list as an individual list and then the pageblocktable or whatever you use will iterate over the specific list.

For example...

<apex:repeat value="{!objectListOfLists}" var="oll">

    <apex:pageBlockTable value="{!oll}" var="acc">

         <apex:column value="{!acc.Name}"/>

    </apex:pageBlockTable>

</apex:repeat>