Ja, das ist eine lästige Situation. Einer der Gründe wieso ich auf Windows entwickle, meine Server allerdings mit Linux laufen.. 
Ansonsten hast du aber nicht viele OptionenWindows der Linux Einstellung anpassenLinux der Windows Einstellung anpassenTabellennamen jeweils umbennenPersönlich finde ich es schöner wenn Gross-/Kleinschreibung unterschieden wird. Aber das ist eher Geschmackssache... Ev. hast du aber auch nur die Möglichkeit, den Windows Server anzupassen und beim Linux Server keinen entsprechend Zugriff. Das würde die Entscheidung ja auch einfacher machen...

Ich hab hier eine Liste mit RENAME Befehlen. Erfahrungsgemäss fehlen dort inzwischen ein paar Tabellen, aber 95% solltest du damit relativ schnell erledigen können.
RENAME TABLE areagroupblocktypes TO AreaGroupBlockTypes;RENAME TABLE areagroups TO AreaGroups;RENAME TABLE areas TO Areas;RENAME TABLE ataddress TO atAddress;RENAME TABLE atboolean TO atBoolean;RENAME TABLE atbooleansettings TO atBooleanSettings;RENAME TABLE atdatetime TO atDateTime;RENAME TABLE atdatetimesettings TO atDateTimeSettings;RENAME TABLE atdefault TO atDefault;RENAME TABLE atfile TO atFile;RENAME TABLE atnumber TO atNumber;RENAME TABLE atselectoptions TO atSelectOptions;RENAME TABLE atselectoptionsselected TO atSelectOptionsSelected;RENAME TABLE atselectsettings TO atSelectSettings;RENAME TABLE attributekeycategories TO AttributeKeyCategories;RENAME TABLE attributekeys TO AttributeKeys;RENAME TABLE attributesetkeys TO AttributeSetKeys;RENAME TABLE attributesets TO AttributeSets;RENAME TABLE attributetypecategories TO AttributeTypeCategories;RENAME TABLE attributetypes TO AttributeTypes;RENAME TABLE attributevalues TO AttributeValues;RENAME TABLE blockrelations TO BlockRelations;RENAME TABLE blocks TO Blocks;RENAME TABLE blocktypes TO BlockTypes;RENAME TABLE btcontentfile TO btContentFile;RENAME TABLE btcontentimage TO btContentImage;RENAME TABLE btcontentlocal TO btContentLocal;RENAME TABLE btexternalform TO btExternalForm;RENAME TABLE btflashcontent TO btFlashContent;RENAME TABLE btform TO btForm;RENAME TABLE btformanswers TO btFormAnswers;RENAME TABLE btformanswerset TO btFormAnswerSet;RENAME TABLE btformquestions TO btFormQuestions;RENAME TABLE btgooglemap TO btGoogleMap;RENAME TABLE btguestbook TO btGuestBook;RENAME TABLE btguestbookentries TO btGuestBookEntries;RENAME TABLE btnavigation TO btNavigation;RENAME TABLE btpagelist TO btPageList;RENAME TABLE btrssdisplay TO btRssDisplay;RENAME TABLE btsearch TO btSearch;RENAME TABLE btslideshow TO btSlideshow;RENAME TABLE btslideshowimg TO btSlideshowImg;RENAME TABLE btsurvey TO btSurvey;RENAME TABLE btsurveyoptions TO btSurveyOptions;RENAME TABLE btsurveyresults TO btSurveyResults;RENAME TABLE btvideo TO btVideo;RENAME TABLE btyoutube TO btYouTube;RENAME TABLE collectionattributevalues TO CollectionAttributeValues;RENAME TABLE collections TO Collections;RENAME TABLE collectionsearchindexattributes TO CollectionSearchIndexAttributes;RENAME TABLE collectionversionblockpermissions TO CollectionVersionBlockPermissions;RENAME TABLE collectionversionblocks TO CollectionVersionBlocks;RENAME TABLE collectionversionblockstyles TO CollectionVersionBlockStyles;RENAME TABLE collectionversions TO CollectionVersions;RENAME TABLE config TO Config;RENAME TABLE dashboardhomepage TO DashboardHomepage;RENAME TABLE downloadstatistics TO DownloadStatistics;RENAME TABLE fileattributevalues TO FileAttributeValues;RENAME TABLE filepermissionfiletypes TO FilePermissionFileTypes;RENAME TABLE filepermissions TO FilePermissions;RENAME TABLE files TO Files;RENAME TABLE filesearchindexattributes TO FileSearchIndexAttributes;RENAME TABLE filesetfiles TO FileSetFiles;RENAME TABLE filesetpermissions TO FileSetPermissions;RENAME TABLE filesets TO FileSets;RENAME TABLE filestoragelocations TO FileStorageLocations;RENAME TABLE fileversionlog TO FileVersionLog;RENAME TABLE fileversions TO FileVersions;RENAME TABLE groups TO Groups;RENAME TABLE jobs TO Jobs;RENAME TABLE jobslog TO JobsLog;RENAME TABLE logs TO Logs;RENAME TABLE mailimporters TO MailImporters;RENAME TABLE mailvalidationhashes TO MailValidationHashes;RENAME TABLE packages TO Packages;RENAME TABLE pagepaths TO PagePaths;RENAME TABLE pagepermissionpagetypes TO PagePermissionPageTypes;RENAME TABLE pagepermissions TO PagePermissions;RENAME TABLE pages TO Pages;RENAME TABLE pagesearchindex TO PageSearchIndex;RENAME TABLE pagestatistics TO PageStatistics;RENAME TABLE pagethemes TO PageThemes;RENAME TABLE pagethemestyles TO PageThemeStyles;RENAME TABLE pagetypeattributes TO PageTypeAttributes;RENAME TABLE pagetypes TO PageTypes;RENAME TABLE pilecontents TO PileContents;RENAME TABLE piles TO Piles;RENAME TABLE signuprequests TO SignupRequests;RENAME TABLE userattributekeys TO UserAttributeKeys;RENAME TABLE userattributevalues TO UserAttributeValues;RENAME TABLE userbannedips TO UserBannedIPs;RENAME TABLE usergroups TO UserGroups;RENAME TABLE useropenids TO UserOpenIDs;RENAME TABLE userprivatemessages TO UserPrivateMessages;RENAME TABLE userprivatemessagesto TO UserPrivateMessagesTo;RENAME TABLE users TO Users;RENAME TABLE usersearchindexattributes TO UserSearchIndexAttributes;RENAME TABLE usersfriends TO UsersFriends;RENAME TABLE uservalidationhashes TO UserValidationHashes;