I ended up creating a Lua function like described here: http://lua-users.org/wiki/SaveTableToFile, to find and remove unneeded keys from the table.

function remove_idx(  tbl, index )

   -- initiate variables for save procedure
   local tables,lookup = { tbl },{ [tbl] = 1 }

   for idx,t in ipairs( tables ) do
      local thandled = {}

      for i,v in ipairs( t ) do
     thandled[i] = true
     local stype = type( v )
     -- only handle value
     if stype == "table" then
        if not lookup[v] then
           table.insert( tables, v )
           lookup[v] = #tables
        end
     else
        if i == index then
           t[i] = nil
           return
        end
     end
      end

      for i,v in pairs( t ) do
     -- escape handled values
     if (not thandled[i]) then

        local flag = 0
        local stype = type( i )
        -- handle index
        if stype == "table" then
           if not lookup[i] then
          table.insert( tables,i )
          lookup[i] = #tables
           end
        else
           flag = 1
           if i == index then
          t[i] = nil
          return
           end
        end

        if flag == 1 then
           stype = type( v )
           -- handle value
           if stype == "table" then
          if not lookup[v] then
             table.insert( tables,v )
             lookup[v] = #tables
          end
           else
          if i == index then
             t[i] = nil
             return
          end
           end
        end

     end
      end
   end
end 

And then inserted my user check and page delete after in libs/web/luasrc/dispatcher.lua dispatch():

if c and c.index then
    local tpl = require "luci.template"

    if util.copcall(tpl.render, "indexer", {}) then
        return true
    end
 end

That's how I remove unneeded pages depending on who is logged in:

    if ctx.authuser == "user" then
            remove_idx(ctx.tree, "packages")
            remove_idx(ctx.tree, "leds")
    end

It is a little bit quick and dirty, but it works. Please note, that direct access by manipulating the URL is still possible.

Update

LuCI2 will provide ACL support und multi-user environment: http://git.openwrt.org/?p=project/luci2/ui.git;a%3Dsummary