Can individual locators in LocatorPane be temporarily disabled?

A simple way to do this is to change the Dynamic so that it updates only the points you want to be editable. Here is a very simple demonstration:

 pts = {{6, 0}, {0, 9}, {3, 0}, {0, 7}};
 updatable = Range@Length@pts;
 Button["Fixate point 3", (updatable = {1, 2, 4})]
 LocatorPane[Dynamic[pts, (pts[[updatable]] = #[[updatable]]) &], 
 Dynamic@Graphics[Point /@ pts, PlotRange -> {{-10, 10}, {-10, 10}}]]

I like @jVincent's approach.

Here is a different approach Overlaying LocatorPanes inside Manipulate :

locPane[Dynamic[pts_], shape_, color_] := 
 LocatorPane[Dynamic[pts], 
 Dynamic@Module[{x = pts[[1, 1]], y = pts[[2, 2]]}, 
 Graphics[{{color, Line[{-m*{x, y}, m*{x, y}}]}, 
  Line[{{x, 0}, {x, y}}], Line[{{x, y}, {0, y}}]}, PlotRange -> m,
  Axes -> True, ImageSize -> {300, 300}]],
 {{{-m, 0}, {m, 0}, {1, 0}}, {{0, -m}, {0, m}, {0, 1}}},
 Appearance -> {shape, shape}];
(* locator apperance graphics *)
redCircle = Graphics[{Red, Table[Circle[{0, 0}, i], {i, 2}]}, ImageSize -> 10];
blueCircle = Graphics[{Blue, Table[Circle[{0, 0}, i], {i, 2}]}, ImageSize -> 10];
grayDisk =  Graphics[{Lighter@Lighter@Gray, Disk[{0, 0}, 2], 
 Gray, Circle[{0, 0}, 3]},  ImageSize -> 10];

Method 1: Overlay two instances of locPane inside a Manipulate

Manipulate[m = 15; 
 Overlay[{
  locPane[Dynamic[pts], Dynamic@If[layer == 1, redCircle, grayDisk], Red], 
  locPane[Dynamic[pts2], Dynamic@If[layer == 2, blueCircle, grayDisk], Blue]},
  All, Dynamic[layer]], 
{{pts, {{6, 0}, {0, 9}}}, ControlType -> None}, 
{{pts2, {{7, 0}, {0, 7}}}, ControlType -> None}, 
{{layer, 1, "layer"}, {1, 2}}]

to get

Method 2: Overlay two instances of locPane inside an EventHandler and Manipulate:

Right-mouse-click toggles between two locator panes:

DynamicModule[{layer = 1}, EventHandler[Manipulate[m = 15;
 Overlay[
{locPane[Dynamic[pts], Dynamic@If[layer == 1, redCircle, grayDisk], Red], 
 locPane[Dynamic[pts2], Dynamic@If[layer == 2, blueCircle, grayDisk], Blue]},
 All, Dynamic[layer]],
{{pts, {{6, 0}, {0, 9}}}, ControlType -> None},
{{pts2, {{7, 0}, {0, 7}}}, ControlType -> None}],
{{"MouseClicked", 2} :> ((layer = layer /. {1 -> 2, 2 -> 1}))}, 
PassEventsDown -> True]]