Use a more less intrusive approach...

bundles/org.eclipse.osgi/META-INF/services/org.osgi.framework.connect.ConnectFrameworkFactory

@@ -1 +1 @@
-org.eclipse.osgi.launch.EquinoxFactory
+org.eclipse.osgi.internal.framework.ConnectFrameworkUtilHelper

bundles/org.eclipse.osgi/container/src/org/eclipse/osgi/internal/framework/ConnectFrameworkUtilHelper.java

@@ -0,0 +1,28 @@
+package org.eclipse.osgi.internal.framework;
+
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Objects;
+import java.util.Optional;
+import java.util.Set;
+import java.util.WeakHashMap;
+import org.osgi.framework.Bundle;
+import org.osgi.framework.connect.FrameworkUtilHelper;
+
+public class ConnectFrameworkUtilHelper implements FrameworkUtilHelper {
+	static final Set<FrameworkUtilHelper> connectHelpers = Collections.newSetFromMap(new WeakHashMap<>());
+
+	@Override
+	public Optional<Bundle> getBundle(Class<?> classFromBundle) {
+		FrameworkUtilHelper[] helpers;
+		synchronized (connectHelpers) {
+			helpers = connectHelpers.toArray(FrameworkUtilHelper[]::new);
+		}
+		return Arrays.stream(helpers).filter(Objects::nonNull)
+				.flatMap(helper -> helper.getBundle(classFromBundle).stream()).findFirst();
+	}
+
+	public static synchronized void add(FrameworkUtilHelper moduleConnector) {
+		connectHelpers.add(moduleConnector);
+	}
+}

bundles/org.eclipse.osgi/container/src/org/eclipse/osgi/internal/framework/EquinoxContainer.java

@@ -57,6 +57,7 @@
 import org.osgi.framework.FrameworkUtil;
 import org.osgi.framework.connect.ConnectContent;
 import org.osgi.framework.connect.ConnectModule;
+import org.osgi.framework.connect.FrameworkUtilHelper;
 import org.osgi.framework.connect.ModuleConnector;
 import org.osgi.util.tracker.ServiceTracker;
 
@@ -154,6 +155,11 @@ private static void initConnectFramework(ModuleConnector moduleConnector, Equino
 		final File fwkStore = new File(configUrl.getPath());
 		@SuppressWarnings({"rawtypes", "unchecked"})
 		Map<String, String> config = (Map) equinoxConfig.getInitialConfig();
+		if (moduleConnector instanceof FrameworkUtilHelper) {
+			// TODO when would this ever be removed? But the SPI has the same problem so
+			// maybe it is okay?
+			ConnectFrameworkUtilHelper.add((FrameworkUtilHelper) moduleConnector);
+		}
 		moduleConnector.initialize(fwkStore, Collections.unmodifiableMap(config));
 	}
 

bundles/org.eclipse.osgi/container/src/org/eclipse/osgi/launch/EquinoxFactory.java

@@ -14,13 +14,7 @@
 package org.eclipse.osgi.launch;
 
 import java.util.Map;
-import java.util.Optional;
-import java.util.Set;
-import java.util.concurrent.ConcurrentHashMap;
-import org.osgi.framework.Bundle;
-import org.osgi.framework.connect.ConnectFramework;
 import org.osgi.framework.connect.ConnectFrameworkFactory;
-import org.osgi.framework.connect.FrameworkUtilHelper;
 import org.osgi.framework.connect.ModuleConnector;
 import org.osgi.framework.launch.Framework;
 import org.osgi.framework.launch.FrameworkFactory;
@@ -29,40 +23,15 @@
  * The framework factory implementation for the Equinox framework.
  * @since 3.5
  */
-public class EquinoxFactory implements FrameworkFactory, ConnectFrameworkFactory, FrameworkUtilHelper {
-
-	static final Set<FrameworkUtilHelper> connectHelpers = ConcurrentHashMap.newKeySet();
+public class EquinoxFactory implements FrameworkFactory, ConnectFrameworkFactory {
 
 	@Override
 	public Framework newFramework(Map<String, String> configuration) {
-		return new Equinox(configuration);
+		return newFramework(configuration, null);
 	}
 
 	@Override
-	public ConnectFramework newFramework(Map<String, String> configuration, ModuleConnector moduleConnector) {
-		return new EquinoxConnect(configuration, moduleConnector);
-	}
-
-	@Override
-	public Optional<Bundle> getBundle(Class<?> classFromBundle) {
-		return connectHelpers.stream().flatMap(helper -> helper.getBundle(classFromBundle).stream()).findFirst();
-	}
-
-	private static final class EquinoxConnect extends Equinox implements ConnectFramework {
-
-		public EquinoxConnect(Map<String, String> configuration, ModuleConnector moduleConnector) {
-			super(configuration, moduleConnector);
-		}
-
-		@Override
-		public void addFrameworkUtilHelper(FrameworkUtilHelper helper) {
-			connectHelpers.add(helper);
-		}
-
-		@Override
-		public void removeFrameworkUtilHelper(FrameworkUtilHelper helper) {
-			connectHelpers.remove(helper);
-		}
-
+	public Framework newFramework(Map<String, String> configuration, ModuleConnector moduleConnector) {
+		return new Equinox(configuration, moduleConnector);
 	}
 }

bundles/org.eclipse.osgi/osgi/src/org/osgi/framework/connect/ConnectFrameworkFactory.java

@@ -74,6 +74,6 @@ public interface ConnectFrameworkFactory {
 	 *             supports permissions.
 	 * @see ModuleConnector
 	 */
-	ConnectFramework newFramework(Map<String, String> configuration,
+	Framework newFramework(Map<String,String> configuration,
 			ModuleConnector moduleConnector);
 }