m2e-wtp can't be disabled for the moment at the workspace level. Please open a feature request at 
As a workaround, you can tell m2e to ignore the m2e-wtp configurator(s) directly in your pom. 
	<profiles>
		<profile>
			<id>m2e</id>
			<!-- This profile is only activated when building in Eclipse with m2e -->
			<activation>
				<property>
					<name>m2e.version</name>
				</property>
			</activation>
			<build>
				<pluginManagement>
					<plugins>
						<plugin>
							<groupId>org.eclipse.m2e</groupId>
							<artifactId>lifecycle-mapping</artifactId>
							<version>1.0.0</version>
							<configuration>
								<lifecycleMappingMetadata>
									<pluginExecutions>
										<pluginExecution>
											<pluginExecutionFilter>
												<groupId>org.apache.maven.plugins</groupId>
												<artifactId>maven-war-plugin</artifactId>
												<versionRange>[2.0.1,)</versionRange>
												<goals>
													<goal>war</goal>
												</goals>
											</pluginExecutionFilter>
											<action>
												<ignore />
											</action>
										</pluginExecution>
									</pluginExecutions>
								</lifecycleMappingMetadata>
							</configuration>
						</plugin>
					</plugins>
				</pluginManagement>
			</build>
		</profile>
	</profiles>